Re: [gmx-users] Error in pdb2gmx
On 4/30/13 2:59 AM, Nikunj Maheshwari wrote: Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro) I used 13. GROMOS 53a6 force field Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu) I get the following options. Which GLUTAMIC ACID type do you want for residue 1 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Both options give the same error as before. The same error occurs for HB1 as well. Will I have to edit the pdb or rtp file? Or any other suggestions? Read the error message again; it tells you what to do. Consider what you're doing - you're supplying a united-atom force field with an all-atom structure. The chosen parameter set doesn't have explicit hydrogens on nonpolar groups. Hence pdb2gmx complains that you're giving it atoms it doesn't understand. Use of -ignh solves this issue, which is precisely what the error message is telling you. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in pdb2gmx
Thanks Justin. I know that using -ignh will solve the problem. But I was just curious because I got the same error message (Fatal error: Atom HD1 in residue HIS 65 was not found in rtp entry HISE with 17 atoms while sorting atoms. ) when I used OPLS, this time it was His 65. So I used -his option in pdb2gmx and got the following options to choose Which HISTIDINE type do you want for residue 65 0. H on ND1 only (HISD) #Works. total charge= -17.000 1. H on NE2 only (HISE) # Error 2. H on ND1 and NE2 (HISH)#Works. total charge= -16.000 3. Coupled to Heme (HIS1) #Works. total charge= -17.000 So shall I go ahead with any of the option except 1, or use -ignh? On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 2:59 AM, Nikunj Maheshwari wrote: Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro) I used 13. GROMOS 53a6 force field Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu) I get the following options. Which GLUTAMIC ACID type do you want for residue 1 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Both options give the same error as before. The same error occurs for HB1 as well. Will I have to edit the pdb or rtp file? Or any other suggestions? Read the error message again; it tells you what to do. Consider what you're doing - you're supplying a united-atom force field with an all-atom structure. The chosen parameter set doesn't have explicit hydrogens on nonpolar groups. Hence pdb2gmx complains that you're giving it atoms it doesn't understand. Use of -ignh solves this issue, which is precisely what the error message is telling you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in pdb2gmx
On 4/30/13 6:10 AM, Nikunj Maheshwari wrote: Thanks Justin. I know that using -ignh will solve the problem. But I was just curious because I got the same error message (Fatal error: Atom HD1 in residue HIS 65 was not found in rtp entry HISE with 17 atoms while sorting atoms. ) when I used OPLS, this time it was His 65. So I used -his option in pdb2gmx and got the following options to choose Which HISTIDINE type do you want for residue 65 0. H on ND1 only (HISD) #Works. total charge= -17.000 1. H on NE2 only (HISE) # Error 2. H on ND1 and NE2 (HISH)#Works. total charge= -16.000 3. Coupled to Heme (HIS1) #Works. total charge= -17.000 So shall I go ahead with any of the option except 1, or use -ignh? In this case, pdb2gmx is detecting that you should have epsilon-protonated histidine at His65, but the proton is at the delta position, so there is a conflict. HISD and HISH work because they both should have a proton on ND1. -Justin On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 2:59 AM, Nikunj Maheshwari wrote: Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro) I used 13. GROMOS 53a6 force field Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu) I get the following options. Which GLUTAMIC ACID type do you want for residue 1 0. Not protonated (charge -1) (GLU) 1. Protonated (charge 0) (GLUH) Both options give the same error as before. The same error occurs for HB1 as well. Will I have to edit the pdb or rtp file? Or any other suggestions? Read the error message again; it tells you what to do. Consider what you're doing - you're supplying a united-atom force field with an all-atom structure. The chosen parameter set doesn't have explicit hydrogens on nonpolar groups. Hence pdb2gmx complains that you're giving it atoms it doesn't understand. Use of -ignh solves this issue, which is precisely what the error message is telling you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in PDB2GMX
sunny mishra wrote: Hi, I am working on HIV-1 Protease with PDB ID 1A8G.pdb. I am trying to convert this protein structure to COARSE GRAINED protein structure and I am done with that but when I am trying to make the topology and conf.gro file from my CG structure of 1A8G.pdb using pdb2gmx it gives me the FATAL ERROR something like this. FATAL ERROR : Incomplete Ring in HIS 69. Now, I am really confused that what will be the solution of this thing. I am also new to GROMACS and I have no idea about the solution of this problem. I would highly appreciate your help for the same. Visit the MARTINI site. They have scripts that generate CG protein topologies. For MARTINI, pdb2gmx is not necessary. -Justin Thanks, Sunny Mishra ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in PDB2GMX
sunny mishra wrote: Hi Justin, Thanks for the expedient reply. I referred MARTINI but after converting 1A8G.pdb to 1A8G_CG.pdb i.e. CG structure of protein I dnt know how to make the topol.top and conf.gro files for that and also I am not able to generate the posre.itp file with this CG structure because it says the fatal error : Incomplete ring of HIS 69. So I don't know how to proceed now and do my simulations. http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html See the Peptides and Proteins section. There are several scripts - a Perl script that writes your topology based on sequence and secondary structure information, and an awk script that converts the structure from atomistic to CG. Note that the awk script is incorrect; each printf line needs to contain $5 between $4 and $6. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in PDB2GMX
sunny mishra wrote: Thats great. I am able to make now my 1A8G.itp file and also the CG structure of protein but now the other problem which is arising is to make the topol.top file and conf.gro file. When I am making this using the command...pdb2gmx -v -f 1A8G_CG.pdb -o conf.gro -p topol.top ..it says choose the forcefield parameter and I am choosing OPLS rather as a matter of fact I have tried all force field parameters and when I run it says FATAL ERROR : Incomplete ring for HIS 69. Do not use pdb2gmx. I have told you that twice. Follow the tutorial on the MARTINI site: http://md.chem.rug.nl/~marrink/MARTINI/Downloads/Tutorial/tutorial.pdf The necessary files are available for download at: http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html -Justin Don't know how to proceed. Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Dear Mark: This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Would you mind telling me how to do that in detail? I tried the following and it doesn't work. diff [ PDM ] ; designation arbitrary, C1 and C2 is -CH3 [ atoms ] SI1 SI 0.3001 C1 opls_069 0.0001 C2 opls_069 0.0001 O1 opls_108-0.3001 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 O1 O1 +SI1 ; Terminal PDMS residue (beginning of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDMB ] [ atoms ] C1opls_069 0.0001 SI1SI 0.3001 C2opls_069 0.0001 C3opls_069 0.0001 O1opls_108-0.3001 [ bonds ] SI1 C1 SI1 C2 SI1 C3 SI1 O1 O1 +SI1 ; Terminal PE residue (end of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDME ] [ atoms ] SI1SI 0.0001 C1opls_069 0.0001 C2opls_069 0.0001 C3opls_069 0.0001 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 C3 diff Thanks a lot in advance! On Mon, May 4, 2009 at 10:15 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Justin A. Lemkul wrote: Then it seems clear to me that your installation of Gromacs is faulty. Have you tried running the test set (available on the wiki site)? If you can describe your computer system (OS, version, compilers used, configuration options, etc.) then perhaps someone on the list can spot a potential pitfall. -Justin Yanmei Song wrote: Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run pdb2gmx using the following two files. I still got the similar error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading pdms2.pdb... Read 13 atoms Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 13 atoms chain #res #atoms 1 ' ' 3 13 All occupancies are one Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx_d, VERSION 4.0.4 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear Mark: This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Would you mind telling me how to do that in detail? On a command line, diff oldfile newfile. Try Googling and reading the man page for diff. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_069 0.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190 158805.0 SI CH3 0.164 293160.0 [ dihedrals ] CH3 SI O SI 3.77 3 0 SI O SI CH3 3.77 3 0 O SI O SI 3.77 3 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't
Re: [gmx-users] Error by pdb2gmx
...@pharm.monash.edu.au wrote: Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx
Re: [gmx-users] Error by pdb2gmx
Justin A. Lemkul wrote: Then it seems clear to me that your installation of Gromacs is faulty. Have you tried running the test set (available on the wiki site)? If you can describe your computer system (OS, version, compilers used, configuration options, etc.) then perhaps someone on the list can spot a potential pitfall. -Justin Yanmei Song wrote: Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run pdb2gmx using the following two files. I still got the similar error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading pdms2.pdb... Read 13 atoms Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 13 atoms chain #res #atoms 1 ' ' 3 13 All occupancies are one Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx_d, VERSION 4.0.4 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3SIO SI dih_PDM_chi1_C_SI_O_SI SI O SI CH3 dih_PDM_chi1_SI_O_SI_C OSIO SI dih_PDM_chi1_O_SI_O_SI The format is the same with other entries. Do you guys think anything wrong with it? Also what does it mean by the error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- what is Source code file: resall.c, line: 289 It seems the problem comes from here. Thanks a lot! On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_069 0.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190 158805.0 SI CH3 0.164 293160.0 [ dihedrals ] CH3 SI O SI 3.77 3 0 SI O SI CH3 3.77 3 0 O SI O SI 3.77 3 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3SIO SI dih_PDM_chi1_C_SI_O_SI SI O SI CH3 dih_PDM_chi1_SI_O_SI_C OSIO SI dih_PDM_chi1_O_SI_O_SI The format is the same with other entries. Do you guys think anything wrong with it? Also what does it mean by the error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- what is Source code file: resall.c, line: 289 It seems the problem comes from here. That is the line of code that is spotting a problem. I think the issue is that, in your original .pdb file, you have dozens of atoms in your polymer chain, all labeled as residue 1. What your .rtp entry says is that a single PDM should contain only three atoms. Since what you are trying to do is make a building block, you will need to do several things: 1. Re-number your .pdb file so that multiple monomers are apparent. 2. Use the + and - characters to indicate connectivity to the next residue and previous residue, respectively. 3. Create separate .rtp entries for terminal groups, as I suggested previously, so that termini are handled correctly (since the -n.tdb and -c.tdb files cannot be used for non-protein). See the amino acid entries for examples on how to use + and - appropriately, or the list archive for examples provided by other users for other polymers (polyethylene is especially common), for example: http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html -Justin Thanks a lot! On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department
Re: [gmx-users] Error by pdb2gmx
Hi, Justin: Thank you so much for your nice help. I will work on that according to your suggestions. On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Hi, Dallas: I added this to the ffoplsaa.rtp [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_069 0.000 1 O opls_108 -0.300 1 [ bonds ] SI O SI CH3 [ dihedrals ] CH3 SI O SI dih_PDM_chi1_C_SI_O_SI SI O SI CH3 dih_PDM_chi1_SI_O_SI_C O SI O SI dih_PDM_chi1_O_SI_O_SI The format is the same with other entries. Do you guys think anything wrong with it? Also what does it mean by the error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- what is Source code file: resall.c, line: 289 It seems the problem comes from here. That is the line of code that is spotting a problem. I think the issue is that, in your original .pdb file, you have dozens of atoms in your polymer chain, all labeled as residue 1. What your .rtp entry says is that a single PDM should contain only three atoms. Since what you are trying to do is make a building block, you will need to do several things: 1. Re-number your .pdb file so that multiple monomers are apparent. 2. Use the + and - characters to indicate connectivity to the next residue and previous residue, respectively. 3. Create separate .rtp entries for terminal groups, as I suggested previously, so that termini are handled correctly (since the -n.tdb and -c.tdb files cannot be used for non-protein). See the amino acid entries for examples on how to use + and - appropriately, or the list archive for examples provided by other users for other polymers (polyethylene is especially common), for example: http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html -Justin Thanks a lot! On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_069 0.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190 158805.0 SI CH3 0.164 293160.0 [ dihedrals ] CH3 SI O SI 3.77 3 0 SI O SI CH3 3.77 3 0 O SI O SI 3.77 3 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] Error by pdb2gmx
Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- what is Source code file: resall.c, line: 289 It seems the problem comes from here. That is the line of code that is spotting a problem. I think the issue is that, in your original .pdb file, you have dozens of atoms in your polymer chain, all labeled as residue 1. What your .rtp entry says is that a single PDM should contain only three atoms. Since what you are trying to do is make a building block, you will need to do several things: 1. Re-number your .pdb file so that multiple monomers are apparent. 2. Use the + and - characters to indicate connectivity to the next residue and previous residue, respectively. 3. Create separate .rtp entries for terminal groups, as I suggested previously, so that termini are handled correctly (since the -n.tdb and -c.tdb files cannot be used for non-protein). See the amino acid entries for examples on how to use + and - appropriately, or the list archive for examples provided by other users for other polymers (polyethylene is especially common), for example: http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html -Justin Thanks a lot! On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3 opls_069 0.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190 158805.0 SI CH3 0.164 293160.0 [ dihedrals ] CH3 SI O SI 3.77 3 0 SI O SI CH3 3.77 3 0 O SI O SI 3.77 3 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Error by pdb2gmx
wrote: That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 9:24 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear Justin and Dallas: Thank you for your help earlier. I made a copy of ffoplsaa.rtp to my working directory and add a new residue to it. Then perform the following command: pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 6 Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat Reading pdms10.pdb... Read 45 atoms Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 45 atoms chain #res #atoms 1 'A' 1 45 All occupancies are one Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: Well that's weird. You should use the diff utility on ffoplsaa.rtp before and after your modifications and see what that tells you. If you've edited it on a Windows machine, then you may have line-ending issues. If so, use dos2unix on the file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Error by pdb2gmx
Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Thursday, 30 April 2009 9:07 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIOSI 3.773 0 SI O SI CH3 3.773 0 OSIOSI 3.773 0 On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is it? :) There is probably something wrong with the .rtp entry you created. If you can post that, perhaps someone can spot it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Department of Chemical Engineering ASU ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 TER -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00 ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00 TER -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
RE: [gmx-users] Error by pdb2gmx
If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00 ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00 ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00 ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00 ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00 ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00 ATOM 44
Re: [gmx-users] Error by pdb2gmx
Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00 ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00 ATOM 38 C74 MOL A 1
Re: [gmx-users] Error by pdb2gmx
Yanmei Song wrote: Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. You will need an entry for the repeat units and the terminal/capping groups. You can make a local copy of the .rtp file and edit it in your working directory; pdb2gmx will then read this copy when processing your structure. -Justin On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00 ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00 ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00 ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00 ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00 ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00 ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00 ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00 ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00 ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00 ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00 ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00 ATOM 36 C69 MOL A 1 3.667
RE: [gmx-users] Error by pdb2gmx
That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 9:24 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Dallas: Thanks for your response. It consists of many repeating units. Do you mean I can write the rtp entry for one repeating unit and give it a residue name. After that I need to insert this into the force field rtp file, right? How can I do that? It seems I can not change the rtp file. Thanks. On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song Sent: Wednesday, 29 April 2009 8:59 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Error by pdb2gmx Dear Justin: Do you have any suggestions on how I can get the itp and gro file for a very long polymer molecules (for example 500 united-atoms), which only consists of Si, O and C atom. I can use PRODRG to generate a short chain. But PRODRG has limitation of atom numbers in a molecule, probably less than 300. So any ideas for building up a long chain based on the short chain? By the way, I already have the force field parameters. Thanks a lot! On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All users: I was trying to set up a long chain polymer system. I got the following PDB file from WebLab. How can I make changes to the file in order to make it as a GROMACS input pdb file. Then I can use pdb2gmx to get the gro, itp and top file. When I perform the pdb2gmx command, I got the error message: Residue 'MOL' not found in residue topology database You can't expect pdb2gmx to be magic. A simple search of the list archives and wiki will turn up the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not _found_in_residue_topology_database -Justin Thank you in advance! REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009 ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00 ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00 ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00 ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00 ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00 ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00 ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00 ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00 ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00 ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00 ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00 ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00 ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00 ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00 ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00 ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00 ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00 ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00 ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00 ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00 ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00 ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00 ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00 ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702
Re: [gmx-users] Error in pdb2gmx
Robert Kretschmer wrote: Dear all, i have a problem while running pdb2gmx. I want to run a md simulation with HIV-ReverseTranscriptase (PDB: 1TVR 1HNV). But in pdb2gmx i get the following error: Fatal error: Incomplete ring in HIS221 I checked HIS221 and found, that it should be an alanine. The .pdb file probably has the name HIS, but some of the atoms are missing. If it is indeed supposed to be an alanine, change the residue name in the .pdb file. If it is supposed to be HIS, however, then you need to re-build the residue using some kind of modeling software. What kann I do? Check for MISSING comments in the header of the .pdb file to be sure of what you are doing. -Justin kind regards robert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
.27_not_found_in_residue_topology_database So your options are: 1. If the ligand is present in the .rtp file, make sure your atom nomenclature corresponds to that of the force field. 2. Remove the ligand and deal with its topology separately (search Google for John Kerrigan's tutorial for enzyme-ligand systems). -Justin vivek sharma wrote: Hi Nahren, Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error. Total mass 28295.072 a.m.u. Total charge 1.000 e Writing topology Processing chain 5 'E' (372 atoms, 9 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: 'NDP' not found in residue topology database, trying to use 'NDPH' --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms while sorting atoms --- and the error for the all atom forcefield were as follow. --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 436 Fatal error: Residue 'NDP' not found in residue topology database --- any advice for this will be of great help for me. Thanx, Vivek 2008/8/12 nahren manuel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On *Tue, 8/12/08, vivek sharma /[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]/* wrote: From: vivek sharma [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
0.1500016 NO2*OA-0.5480016 NH2* H 0.3980016 NC3* CH1 0.1500017 NO3*OA-0.5480017 NH3* H 0.3980017 are those file indicating some error like atom name are different in two files, is this the reason for my error or I have to think in some other way. Any advice would be of great help. With Thanx, Vivek 2008/8/13 vivek sharma [EMAIL PROTECTED] Hi Nahren, Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error. Total mass 28295.072 a.m.u. Total charge 1.000 e Writing topology Processing chain 5 'E' (372 atoms, 9 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: 'NDP' not found in residue topology database, trying to use 'NDPH' --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms while sorting atoms --- and the error for the all atom forcefield were as follow. --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 436 Fatal error: Residue 'NDP' not found in residue topology database --- any advice for this will be of great help for me. Thanx, Vivek 2008/8/12 nahren manuel [EMAIL PROTECTED] Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On *Tue, 8/12/08, vivek sharma [EMAIL PROTECTED]* wrote: From: vivek sharma [EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list[EMAIL PROTECTED]://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Hi Justin, Thanx for your suggestion. But, I am not getting how to do correction in those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my simulation. I am not getting what is happening in the simulation...:(...:( kindly suggest. With Thanx, Vivek 2008/8/13 Justin A. Lemkul [EMAIL PROTECTED] There are two potential solutions to this error. For background, refer to: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database So your options are: 1. If the ligand is present in the .rtp file, make sure your atom nomenclature corresponds to that of the force field. 2. Remove the ligand and deal with its topology separately (search Google for John Kerrigan's tutorial for enzyme-ligand systems). -Justin vivek sharma wrote: Hi Nahren, Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error. Total mass 28295.072 a.m.u. Total charge 1.000 e Writing topology Processing chain 5 'E' (372 atoms, 9 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: 'NDP' not found in residue topology database, trying to use 'NDPH' --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms while sorting atoms --- and the error for the all atom forcefield were as follow. --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 436 Fatal error: Residue 'NDP' not found in residue topology database --- any advice for this will be of great help for me. Thanx, Vivek 2008/8/12 nahren manuel [EMAIL PROTECTED] mailto: [EMAIL PROTECTED] Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On *Tue, 8/12/08, vivek sharma /[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]/* wrote: From: vivek sharma [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma wrote: Hi Justin, Thanx for your suggestion. But, I am not getting how to do correction in those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my simulation. I am not getting what is happening in the simulation...:(...:( kindly suggest. I'm guessing that NDP is the NADPH cofactor, which in Gromos96 language is called NDPH (that's what pdb2gmx is trying to call, it as well). What's happening is you've got the atoms present for NADPH, but the force field simply has different names for the atoms. The simple fix is to re-name the atoms in the .pdb file according to how they appear in the .rtp entry for NADPH (called NDPH). For example, the two phosphorus atoms in the phosphodiester between the adenosine and nicotinamide moieties are called AP and NP. AP corresponds to the P atom in the phosphate donated by the adenoside system; NP corresponds to the P atom from the nicotinamide phosphate. You've got an atom called PA instead, which is probably equivalent to AP (but do check, because that's just a guess from my end). -Justin With Thanx, Vivek 2008/8/13 Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] There are two potential solutions to this error. For background, refer to: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database So your options are: 1. If the ligand is present in the .rtp file, make sure your atom nomenclature corresponds to that of the force field. 2. Remove the ligand and deal with its topology separately (search Google for John Kerrigan's tutorial for enzyme-ligand systems). -Justin vivek sharma wrote: Hi Nahren, Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error. Total mass 28295.072 a.m.u. Total charge 1.000 e Writing topology Processing chain 5 'E' (372 atoms, 9 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: 'NDP' not found in residue topology database, trying to use 'NDPH' --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms while sorting atoms --- and the error for the all atom forcefield were as follow. --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 436 Fatal error: Residue 'NDP' not found in residue topology database --- any advice for this will be of great help for me. Thanx, Vivek 2008/8/12 nahren manuel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On *Tue, 8/12/08, vivek sharma /[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]/* wrote: From: vivek sharma [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st
Re: [gmx-users] Error in pdb2gmx
vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 878 Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 1034, atom 7961) --- as I am new to this field. I'm finding it very difficult to find the reason and rectify it. Any suggestion would be of great help.. This is a limitation in pdb2gmx. It expects the atoms in the chain A to be in sequence in the pdb file. You can manually sort the pdb file on the chain identifier. With Thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx
Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 878 Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 1034, atom 7961) --- as I am new to this field. I'm finding it very difficult to find the reason and rectify it. Any suggestion would be of great help.. This is a limitation in pdb2gmx. It expects the atoms in the chain A to be in sequence in the pdb file. You can manually sort the pdb file on the chain identifier. With Thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx
vivek sharma wrote: Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. with a text editor, like emacs, notepad or whatever. With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 878 Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 1034, atom 7961) --- as I am new to this field. I'm finding it very difficult to find the reason and rectify it. Any suggestion would be of great help.. This is a limitation in pdb2gmx. It expects the atoms in the chain A to be in sequence in the pdb file. You can manually sort the pdb file on the chain identifier. With Thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. Sounds like the crystal structure has missing atoms. You'll need to reconstruct the missing portions with a modeling program like DeepView or Modeller. -Justin With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx
Hi david, Thanx again, but I want to ask what changes need to be done there in such cases. With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. with a text editor, like emacs, notepad or whatever. With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] mailto: [EMAIL PROTECTED] vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 878 Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 1034, atom 7961) --- as I am new to this field. I'm finding it very difficult to find the reason and rectify it. Any suggestion would be of great help.. This is a limitation in pdb2gmx. It expects the atoms in the chain A to be in sequence in the pdb file. You can manually sort the pdb file on the chain identifier. With Thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx
vivek sharma wrote: Hi david, Thanx again, but I want to ask what changes need to be done there in such cases. The chain identifier needs to be continuous. That is, if you have atoms with chain identifiers like: A A B A C A A they should be re-written as: A A A A A B C This can be accomplished with some work in a simple text editor. -Justin With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. with a text editor, like emacs, notepad or whatever. With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 878 Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 1034, atom 7961) --- as I am new to this field. I'm finding it very difficult to find the reason and rectify it. Any suggestion would be of great help.. This is a limitation in pdb2gmx. It expects the atoms in the chain A to be in sequence in the pdb file. You can manually sort the pdb file on the chain identifier. With Thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
If atoms are missing in the sidechains of your protein, you can try a program like scwrl3 to rebuild all or some of the sidechains. This will give you complete sidechains in sort of reasonable positions. Cheers /Per 12 aug 2008 kl. 15.04 skrev vivek sharma: Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On Tue, 8/12/08, vivek sharma [EMAIL PROTECTED] wrote: From: vivek sharma [EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. ... ... ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx
Well,
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- sorted.pdb
sort of seems to do the trick. But it will place the chainless things first.
Hope it helps,
Tsjerk
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote:
vivek sharma wrote:
Hi david,
Thanx again, but I want to ask what changes need to be done there in such
cases.
The chain identifier needs to be continuous. That is, if you have atoms
with chain identifiers like:
A
A
B
A
C
A
A
they should be re-written as:
A
A
A
A
A
B
C
This can be accomplished with some work in a simple text editor.
-Justin
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hi David,
Thanks for the quick reply. My apologies for asking you again a
silly doubt as, I am doing this all for the first time. It will
be of great help if you can tell me how to do such correction
manually.
with a text editor, like emacs, notepad or whatever.
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hello there,
I am trying to run pdb2gmx on 3bzu.pdb file and got the
following error
Opening library file /usr/share/gromacs/top/
ffG43b1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Reading 3bzu.pdb...
WARNING: all CONECT records are ignored
Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
BETA-HSD1', 8581 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
---
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 878
Fatal error:
Chain identifier 'A' was used in two non-sequential blocks
(residue 1034, atom 7961)
---
as I am new to this field. I'm finding it very difficult to
find the reason and rectify it.
Any suggestion would be of great help..
This is a limitation in pdb2gmx. It expects the atoms in the
chain
A to be in sequence in the pdb file. You can manually sort
the pdb
file on the chain identifier.
With Thanx,
Vivek
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Please search the archive at http://www.gromacs.org/search
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Please don't post (un)subscribe requests to the list. Use the
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mailto:[EMAIL PROTECTED].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error in pdb2gmx
Thanx David and Tsjerk,
I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
sorted pdb file was giving the following error.
Sorting it all out...
Opening library file /usr/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
Processing chain 1 'A' (2108 atoms, 601 residues)
There are 393 donors and 383 acceptors
There are 533 hydrogen bonds
---
Program pdb2gmx, VERSION 3.3.3
Source code file: hizzie.c, line: 267
Fatal error:
Incomplete ring in HIS194
---
Here I am attaching the sorted.pdb file, it is having some amino acids
inserted between some other amino acid as below
text from sorted pdb shows GLN and GLU are inserted in HIS
ATOM793 CD2 PHE A 129 -1.911 -9.897 3.599 1.00 43.21
C
ATOM794 CE1 PHE A 129 -1.839 -11.242 5.997 1.00 41.19
C
ATOM795 CE2 PHE A 129 -2.911 -10.794 3.911 1.00 41.19
C
ATOM796 CZ PHE A 129 -2.874 -11.465 5.104 1.00 42.09
C
ATOM797 N HIS A 130 1.739 -11.572 3.175 1.00 54.14
N
ATOM798 CA HIS A 130 1.520 -12.688 2.246 1.00 55.63
C
ATOM799 C HIS A 130 0.177 -13.421 2.474 1.00 55.34
C
ATOM 79 CD GLN A 33 8.099 10.312 47.238 1.00 69.55
C
ATOM 7 CD GLU A 25 -0.646 19.004 39.566 1.00 87.49
C
ATOM800 O HIS A 130 -0.859 -13.049 1.913 1.00 56.40
O
ATOM801 CB HIS A 130 2.726 -13.659 2.201 1.00 56.33
C
ATOM802 CG HIS A 130 3.542 -13.730 3.467 1.00 58.59
C
ATOM803 ND1 HIS A 130 4.249 -12.655 3.970 1.00 60.95
N
ATOM804 CD2 HIS A 130 3.828 -14.777 4.284 1.00 59.58
C
ATOM805 CE1 HIS A 130 4.895 -13.022 5.066 1.00 60.24
C
ATOM806 NE2 HIS A 130 4.657 -14.305 5.279 1.00 60.16
N
ATOM807 N ASP A 131 0.207 -14.462 3.285 1.00 54.76
N
ATOM808 CA ASP A 131 -0.954 -15.320 3.512 1.00 54.01
C
ATOM809 C ASP A 131 -1.040 -15.548 4.997 1.00 51.90
C
ATOM 80 OE1 GLN A 33 7.692 11.421 46.868 1.00 70.33
O
Kindly suggest any way to correct the .pdb file so that it can be converted
to .gro file
With Thanx,
Vivek
2008/8/12 Tsjerk Wassenaar [EMAIL PROTECTED]
Well,
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- sorted.pdb
sort of seems to do the trick. But it will place the chainless things
first.
Hope it helps,
Tsjerk
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote:
vivek sharma wrote:
Hi david,
Thanx again, but I want to ask what changes need to be done there in
such
cases.
The chain identifier needs to be continuous. That is, if you have atoms
with chain identifiers like:
A
A
B
A
C
A
A
they should be re-written as:
A
A
A
A
A
B
C
This can be accomplished with some work in a simple text editor.
-Justin
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hi David,
Thanks for the quick reply. My apologies for asking you again a
silly doubt as, I am doing this all for the first time. It will
be of great help if you can tell me how to do such correction
manually.
with a text editor, like emacs, notepad or whatever.
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hello there,
I am trying to run pdb2gmx on 3bzu.pdb file and got the
following error
Opening library file /usr/share/gromacs/top/
ffG43b1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Reading 3bzu.pdb...
WARNING: all CONECT records are ignored
Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
BETA-HSD1', 8581 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
---
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 878
Fatal error:
Chain identifier 'A' was used in two non-sequential blocks
(residue 1034, atom 7961)
---
as I am new to this field. I'm finding it very difficult
to
find the reason and rectify it.
Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Hi Nahren, Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error. Total mass 28295.072 a.m.u. Total charge 1.000 e Writing topology Processing chain 5 'E' (372 atoms, 9 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Warning: 'NDP' not found in residue topology database, trying to use 'NDPH' --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms while sorting atoms --- and the error for the all atom forcefield were as follow. --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 436 Fatal error: Residue 'NDP' not found in residue topology database --- any advice for this will be of great help for me. Thanx, Vivek 2008/8/12 nahren manuel [EMAIL PROTECTED] Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs. nahren --- On *Tue, 8/12/08, vivek sharma [EMAIL PROTECTED]* wrote: From: vivek sharma [EMAIL PROTECTED] Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, August 12, 2008, 6:34 PM Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel [EMAIL PROTECTED] vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom --- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens --- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. You have an incorrect pdb file. An atom is missing. You have to fix it yourself. With thanx, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list[EMAIL PROTECTED]://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http
Re: [gmx-users] Error in pdb2gmx
Hi Vivek,
Sorry, I should've been more careful. Sorting will obviously take the
rest of the line in account. I'll send a proper solution in a few
moments...
Cheers,
Tsjerk
On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma
[EMAIL PROTECTED] wrote:
Thanx David and Tsjerk,
I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
sorted pdb file was giving the following error.
Sorting it all out...
Opening library file /usr/share/gromacs/top/
ffG43a1.hdb
Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
Processing chain 1 'A' (2108 atoms, 601 residues)
There are 393 donors and 383 acceptors
There are 533 hydrogen bonds
---
Program pdb2gmx, VERSION 3.3.3
Source code file: hizzie.c, line: 267
Fatal error:
Incomplete ring in HIS194
---
Here I am attaching the sorted.pdb file, it is having some amino acids
inserted between some other amino acid as below
text from sorted pdb shows GLN and GLU are inserted in HIS
ATOM793 CD2 PHE A 129 -1.911 -9.897 3.599 1.00 43.21
C
ATOM794 CE1 PHE A 129 -1.839 -11.242 5.997 1.00 41.19
C
ATOM795 CE2 PHE A 129 -2.911 -10.794 3.911 1.00 41.19
C
ATOM796 CZ PHE A 129 -2.874 -11.465 5.104 1.00 42.09
C
ATOM797 N HIS A 130 1.739 -11.572 3.175 1.00 54.14
N
ATOM798 CA HIS A 130 1.520 -12.688 2.246 1.00 55.63
C
ATOM799 C HIS A 130 0.177 -13.421 2.474 1.00 55.34
C
ATOM 79 CD GLN A 33 8.099 10.312 47.238 1.00 69.55
C
ATOM 7 CD GLU A 25 -0.646 19.004 39.566 1.00 87.49
C
ATOM800 O HIS A 130 -0.859 -13.049 1.913 1.00 56.40
O
ATOM801 CB HIS A 130 2.726 -13.659 2.201 1.00 56.33
C
ATOM802 CG HIS A 130 3.542 -13.730 3.467 1.00 58.59
C
ATOM803 ND1 HIS A 130 4.249 -12.655 3.970 1.00 60.95
N
ATOM804 CD2 HIS A 130 3.828 -14.777 4.284 1.00 59.58
C
ATOM805 CE1 HIS A 130 4.895 -13.022 5.066 1.00 60.24
C
ATOM806 NE2 HIS A 130 4.657 -14.305 5.279 1.00 60.16
N
ATOM807 N ASP A 131 0.207 -14.462 3.285 1.00 54.76
N
ATOM808 CA ASP A 131 -0.954 -15.320 3.512 1.00 54.01
C
ATOM809 C ASP A 131 -1.040 -15.548 4.997 1.00 51.90
C
ATOM 80 OE1 GLN A 33 7.692 11.421 46.868 1.00 70.33
O
Kindly suggest any way to correct the .pdb file so that it can be converted
to .gro file
With Thanx,
Vivek
2008/8/12 Tsjerk Wassenaar [EMAIL PROTECTED]
Well,
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- sorted.pdb
sort of seems to do the trick. But it will place the chainless things
first.
Hope it helps,
Tsjerk
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote:
vivek sharma wrote:
Hi david,
Thanx again, but I want to ask what changes need to be done there in
such
cases.
The chain identifier needs to be continuous. That is, if you have atoms
with chain identifiers like:
A
A
B
A
C
A
A
they should be re-written as:
A
A
A
A
A
B
C
This can be accomplished with some work in a simple text editor.
-Justin
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hi David,
Thanks for the quick reply. My apologies for asking you again a
silly doubt as, I am doing this all for the first time. It will
be of great help if you can tell me how to do such correction
manually.
with a text editor, like emacs, notepad or whatever.
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hello there,
I am trying to run pdb2gmx on 3bzu.pdb file and got the
following error
Opening library file /usr/share/gromacs/top/
ffG43b1.rtp
Opening library file
/usr/share/gromacs/top/aminoacids.dat
Reading 3bzu.pdb...
WARNING: all CONECT records are ignored
Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
BETA-HSD1', 8581 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
---
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 878
Fatal error:
Re: [gmx-users] Error in pdb2gmx
Hi Vivek,
I downloaded 3bzu.pdb and ran the sorting on it as I described before
(sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
3bzu.pdb | sort | cut -b 2-), and it worked perfectly for me. I don't
see how you'd end up with some atoms inbetween other residues. It
seems as if the sorting counts space number.
I do see another problem though, which is more fundamental to your
initial problem. The resason for not having consecutive chain
identifiers is that all hetatms are placed at the end of the atom
listing. If these hetatm residues are part of the same molecule, you'd
be on the right route (sorting and running pdb2gmx), but you'll have
to make sure you have building block descriptions. If these are not
part of the same molecule, you better remove them from the file before
running pdb2gmx, make topology include files for each separate
molecule and combine these later on. If you don't understand what I'm
talking about, don't do it; pick another protein.
Cheers,
Tsjerk
On Wed, Aug 13, 2008 at 7:37 AM, Tsjerk Wassenaar [EMAIL PROTECTED] wrote:
Hi Vivek,
Sorry, I should've been more careful. Sorting will obviously take the
rest of the line in account. I'll send a proper solution in a few
moments...
Cheers,
Tsjerk
On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma
[EMAIL PROTECTED] wrote:
Thanx David and Tsjerk,
I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
sorted pdb file was giving the following error.
Sorting it all out...
Opening library file /usr/share/gromacs/top/
ffG43a1.hdb
Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
Processing chain 1 'A' (2108 atoms, 601 residues)
There are 393 donors and 383 acceptors
There are 533 hydrogen bonds
---
Program pdb2gmx, VERSION 3.3.3
Source code file: hizzie.c, line: 267
Fatal error:
Incomplete ring in HIS194
---
Here I am attaching the sorted.pdb file, it is having some amino acids
inserted between some other amino acid as below
text from sorted pdb shows GLN and GLU are inserted in HIS
ATOM793 CD2 PHE A 129 -1.911 -9.897 3.599 1.00 43.21
C
ATOM794 CE1 PHE A 129 -1.839 -11.242 5.997 1.00 41.19
C
ATOM795 CE2 PHE A 129 -2.911 -10.794 3.911 1.00 41.19
C
ATOM796 CZ PHE A 129 -2.874 -11.465 5.104 1.00 42.09
C
ATOM797 N HIS A 130 1.739 -11.572 3.175 1.00 54.14
N
ATOM798 CA HIS A 130 1.520 -12.688 2.246 1.00 55.63
C
ATOM799 C HIS A 130 0.177 -13.421 2.474 1.00 55.34
C
ATOM 79 CD GLN A 33 8.099 10.312 47.238 1.00 69.55
C
ATOM 7 CD GLU A 25 -0.646 19.004 39.566 1.00 87.49
C
ATOM800 O HIS A 130 -0.859 -13.049 1.913 1.00 56.40
O
ATOM801 CB HIS A 130 2.726 -13.659 2.201 1.00 56.33
C
ATOM802 CG HIS A 130 3.542 -13.730 3.467 1.00 58.59
C
ATOM803 ND1 HIS A 130 4.249 -12.655 3.970 1.00 60.95
N
ATOM804 CD2 HIS A 130 3.828 -14.777 4.284 1.00 59.58
C
ATOM805 CE1 HIS A 130 4.895 -13.022 5.066 1.00 60.24
C
ATOM806 NE2 HIS A 130 4.657 -14.305 5.279 1.00 60.16
N
ATOM807 N ASP A 131 0.207 -14.462 3.285 1.00 54.76
N
ATOM808 CA ASP A 131 -0.954 -15.320 3.512 1.00 54.01
C
ATOM809 C ASP A 131 -1.040 -15.548 4.997 1.00 51.90
C
ATOM 80 OE1 GLN A 33 7.692 11.421 46.868 1.00 70.33
O
Kindly suggest any way to correct the .pdb file so that it can be converted
to .gro file
With Thanx,
Vivek
2008/8/12 Tsjerk Wassenaar [EMAIL PROTECTED]
Well,
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- sorted.pdb
sort of seems to do the trick. But it will place the chainless things
first.
Hope it helps,
Tsjerk
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote:
vivek sharma wrote:
Hi david,
Thanx again, but I want to ask what changes need to be done there in
such
cases.
The chain identifier needs to be continuous. That is, if you have atoms
with chain identifiers like:
A
A
B
A
C
A
A
they should be re-written as:
A
A
A
A
A
B
C
This can be accomplished with some work in a simple text editor.
-Justin
With Thanx,
Vivek
2008/8/12 David van der Spoel [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
vivek sharma wrote:
Hi David,
Thanks for the quick reply. My apologies for asking you again a
silly doubt as, I am doing this all for the first time. It will
be of great help if you can tell me how to do such correction
manually.
with a text editor, like emacs, notepad or whatever.
With Thanx,
Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN [EMAIL PROTECTED]: I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :) Thank you Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http
Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN [EMAIL PROTECTED]: Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :) So have I got it correct that you truncated the N-terminus originally, and are now adding residues back? It still suggests to me that you've generated a poor starting structure; the nomenclature should not be causing the issue. Identify which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate them with a viewer (VMD, etc). Likely the model you've constructed has some non-physical attributes. -Justin Thank you Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use
Re: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Justin, thank you very much for your attention. This is totally my fault. After putting N to the first residue, the column that indicates the coordinates has been flipped to the right. So, the first numbers could not be read by pdb2gmx. That is the source of the problem. However, thank you again. -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 17:41:50 -0400 Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about the nomenclature of the N terminus. I read things in the link, searched the web and made some discussion with my friend, but I could not find the source of the error :) So have I got it correct that you truncated the N-terminus originally, and are now adding residues back? It still suggests to me that you've generated a poor starting structure; the nomenclature should not be causing the issue. Identify which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate them with a viewer (VMD, etc). Likely the model you've constructed has some non-physical attributes. -Justin Thank you Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 15:25:11 -0400 Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having long bonds. It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force on atoms. Alright, that makes more sense. You didn't say before that you couldn't resolve the long bonds by minimization. It seemed that you were asking again about the N-terminal nomenclature. It sounds like your starting structure has problems, but without knowing more I can't comment on that. Is it something you've built, something from the RCSB, etc? Have a look at your structure and the mdrun output (md.log, in particular) to see if you can determine where things are falling apart based on specific warnings (LINCS, etc.) -Justin -Original Message- From: Justin A. Lemkul [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 31 Mar 2008 14:42:55 -0400 Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS Quoting OZGE ENGIN [EMAIL PROTECTED]: Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., NGLN), and likewise for C-terminal residues, CXXX. This is in the documentation from the AMBER ports at the link you cite above, and the link I already provided you. So what's the problem? -Justin Thanks in advance Ozge Engin = Computational Science Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in pdb2gmx
Dmitriy Golubobsky wrote: Please, give an adive. I've add new residues to ffoplsaa.rtp build pdb file. and try to convert it to gromacs format. under WindowsXP, using GROMACS 3.2.1 everyting is OK. but, when i did the same comman under GROMACS 3.3.1 (SuSE), i've got an error: Read 4904 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 258 residues with 4904 atoms chain #res #atoms 1 ' ' 258 4904 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp --- Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- These Gromacs Guys Really Rock (P.J. Meulenhoff) What I'm doing wrong? This is only a guess, but if your .rtp file uses Windows line-endings and pdb2gmx is sensitive to that, you might see such a problem. Use dos2unix on all your ex-Windows files and see how you go. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in pdb2gmx step
Check you pdb file and see if the chain identifier A occurs at different places in the file. Pdb2gmx expects a chain to be continous, and if it isn't, it gets confused. If you have several chains, rename them accordingly. Cheers /Per Annie Albin wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Per Larsson PhD Student Stockholm Bioinformatics Center +46 (0) 8 55378577 +46 (0) 733 461467 [EMAIL PROTECTED] www.sbc.su.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in pdb2gmx step
Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in pdb2gmx step
Well thank you.Yes I did find a region in which chain identifier 'A' was repeating, this corresponded to the HETATM CO, so i tried removing the chain identifier in one case and in another one I tried shifting it to the correspoding chain, but in both cases i got the following error Fatal error: Residue 'CO' not found in residue topology database. Will be glad to hear any suggestions. Is there any other way in GROMACS to handle proteins with metal ions in it? Thank You, Annie Albin. On 3/31/06, MGiò [EMAIL PROTECTED] wrote: Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in pdb2gmx step
That means that the CO ion type is not described by the forcefield you are using, check the .rtp file of your force field or the ions.itp file in the gromacs/top directory. anyhow be careful not to make any confusion between the chain identifier, which is a 1 character id, and the residue name. Are you sure you're not shifting the columns of your pdb when deleting the chain identifier (chain A shoud be replaced by a blank)? MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Well thank you.Yes I did find a region in which chain identifier 'A' was repeating, this corresponded to the HETATM CO, so i tried removing the chain identifier in one case and in another one I tried shifting it to the correspoding chain, but in both cases i got the following error Fatal error: Residue 'CO' not found in residue topology database. Will be glad to hear any suggestions. Is there any other way in GROMACS to handle proteins with metal ions in it? Thank You, Annie Albin. On 3/31/06, MGiò [EMAIL PROTECTED] wrote: Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin [EMAIL PROTECTED] wrote: Dear all, I faced a problem in the pdb2gmx step as i got this following error message, Fatal error: Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013) As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help. Thank you, Annie Albin. ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
