Re: [gmx-users] pdb files from trajectory
Hi Shima, You need to give a reference structure with the -s option. Otherwise the program assumes you mean to use topol.tpr, which isn't present. Cheers, Tsjerk On Sun, Jul 7, 2013 at 11:51 AM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Dear gmx users, I' d like to get pdb files from trajectory, then used the trjconv, # trjconv -f trajout.xtc -o out.pdb -sep It gives fatal error as this: Can not open file: topol.tpr Sincerely, Shima -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] pdb files from trajectory
Dear Shima What is the name of your .tpr file? If you had not chosen any name for it, Gromacs will generate a topol.tpr for you and in my idea this error will not occur, if not, you have to mention your file (e.g. Filename.tpr) explicitely in your command line! I hope this help you Best On Sun, Jul 7, 2013 at 2:21 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I' d like to get pdb files from trajectory, then used the trjconv, # trjconv -f trajout.xtc -o out.pdb -sep It gives fatal error as this: Can not open file: topol.tpr Sincerely, Shima -- 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 -- 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] pdb files using hex resid
On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Mark -- 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] pdb files using hex resid
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Is there a configure flag that controls this? and do you mean dlpolyplugin.so ? Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] pdb files using hex resid
On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? Script g_select? Mark -- 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] pdb files using hex resid
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? Script g_select? That sounds good. Although I may have a workaround by altering my procedure. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] pdb files using hex resid
On 4/01/2012 2:19 PM, Peter C. Lai wrote: On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Sorry, dlopen is the mechanism that allows the executing code to see if a dynamic link library contains a function that delivers the required functionality. So it's just a matter of having the VMD stuff in the dynamic linking path. Mark -- 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] pdb files using hex resid
On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote: On 4/01/2012 2:19 PM, Peter C. Lai wrote: On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Sorry, dlopen is the mechanism that allows the executing code to see if a dynamic link library contains a function that delivers the required functionality. So it's just a matter of having the VMD stuff in the dynamic linking path. Well I added -I/usr/local/vmd/plugins/include to CPPFLAGS and -L/usr/local/vmd/plugins/FREEBSDAMD64/molfile to LDFLAGS and the recompiled editconf is still uable to properly parse the vmd-style pdb Oh well -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] pdb files using hex resid
On 4/01/2012 2:59 PM, Peter C. Lai wrote: On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote: On 4/01/2012 2:19 PM, Peter C. Lai wrote: On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Sorry, dlopen is the mechanism that allows the executing code to see if a dynamic link library contains a function that delivers the required functionality. So it's just a matter of having the VMD stuff in the dynamic linking path. Well I added -I/usr/local/vmd/plugins/include to CPPFLAGS and -L/usr/local/vmd/plugins/FREEBSDAMD64/molfile to LDFLAGS and the recompiled editconf is still uable to properly parse the vmd-style pdb Sure... presumably the VMD stuff is only invoked for file types for which there is not native support. Note that I suggested using some other intermediate format, not trying to read the non-standard PDB. Mark -- 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] pdb files
Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On Sat, 3/7/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing list 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 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] pdb files
Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ? Thanks in advance --- On Thu, 3/12/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, March 12, 2009, 12:11 PM oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? You're stuck either writing an .rtp entry for use with pdb2gmx, or writing the .itp yourself. -Justin Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On *Sat, 3/7/09, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=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 /mc/compose?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
Re: [gmx-users] pdb files
oguz gurbulak wrote: Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ? Read the manual, section 5.6.1. -Justin Thanks in advance --- On *Thu, 3/12/09, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, March 12, 2009, 12:11 PM oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? You're stuck either writing an .rtp entry for use with pdb2gmx, or writing the .itp yourself. -Justin Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On *Sat, 3/7/09, Justin A. Lemkul /jalem...@vt.edu /mc/compose?to=jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu /mc/compose?to=jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com /mc/compose?to=gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_AN Molecule_BN SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org /mc/compose?to=gmx-us...@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://www.gromacs.org/mailman
Re: [gmx-users] pdb files
oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_AN Molecule_BN SOL N (then whatever ions you need, if any) -Justin Sincerely ___ 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] pdb files
Sagittarius wrote: Dear Gromacs users, Could you please help me to find pdb files for glyceric acid esters cyanamide phosphatidylcholine glyceroyl thioesters tetrose polyglyceric acid hemiacetal Thank you in advance You build these yourself using a molecule building program. I don't know of any good free ones, but maybe some others on this list do. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb files
Dear Mark Abraham Thank you very much for your help. Could you please help me to find such a not free molecule building program. Maybe it will be useful anyway somehow. Thank you in advance. Mark Abraham [EMAIL PROTECTED] wrote: Sagittarius wrote: Dear Gromacs users, Could you please help me to find pdb files for glyceric acid esters cyanamide phosphatidylcholine glyceroyl thioesters tetrose polyglyceric acid hemiacetal Thank you in advance You build these yourself using a molecule building program. I don't know of any good free ones, but maybe some others on this list do. Mark ___ gmx-users mailing list 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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search.___ 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] pdb files
Dear Mark Abraham Thank you very much for your help. Could you please help me to find such a not free molecule building program. Maybe it will be useful anyway somehow. Start with a Google search. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pdb files
This site can have some: http://alpha2.bmc.uu.se/hicup/ Welcome to HIC-Up, the Hetero-compound Information Centre - Uppsala, a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds (small molecules). Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] pdb files
Dallas B. Warren wrote: This site can have some: http://alpha2.bmc.uu.se/hicup/ Welcome to HIC-Up, the Hetero-compound Information Centre - Uppsala, a freely accessible resource for structural biologists who are dealing dealing with hetero-compounds (small molecules). otherwise molden or prodrg will do the trick. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
