[gmx-users] dssp works fine, but do_dssp gives fatal error
Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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] dssp works fine, but do_dssp gives fatal error
Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 -- 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] dssp works fine, but do_dssp gives fatal error
The location of dssp is /usr/local/bin/dssp On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Right. And what is its location? On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 -- 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 -- 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] dssp works fine, but do_dssp gives fatal error
Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 -- 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 -- 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] dssp works fine, but do_dssp gives fatal error
My current Gromacs version is 4.5.5 I think using the first option will be easy and quick. On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund er...@xray.bmc.uu.se wrote: You have (at least) two easy options. 1) Install old_dssp that is available through the dssp web page. 2) Install a newer version of gromacs than you have at the moment. What version do you currently use? Erik On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 -- 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 -- 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 -- 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] How to visualize .gro file without .tpr file
Alternatively, you can use editconf -f (tpr file) -o (pdb file) to convert .gro to .pdb, and then use the visualization tools such as Pymol to view it. On Tue, May 21, 2013 at 1:01 AM, Vishal Kumar Jaiswal vishal3...@gmail.comwrote: Vmd can visualise a GRO file directly without .tpr . I use it to visualise gro files On Tue, May 21, 2013 at 12:59 AM, Bao Kai paeanb...@gmail.com wrote: HI, all, I have a small question here. I usually use ngmx to visualize the .gro or .trr file with a .tpr file. While after simulation, I use editconf to generate a new .gro file. Then I failed to visualize the new .gro file since the .tpr file did not work for the new .gro file now. I wonder if there is some other method to visualize the .gro file? Thank you very much. Best Regards, Kai -- 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 -- 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] Large number of solvent molecules
Dear all, I am trying to see the folding of a 89 aa peptide. So I am setting up the system from linear conformation. I gave the following commands to build the box and add the solvent molecules. editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro Reading solute configuration Go Rough, Oppose Many Angry Chinese Serial killers Containing 1440 atoms in 89 residues Initialising van der waals distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC- MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 18x18x13 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 909792 residues Calculating Overlap... box_margin = 0.315 Removed 324522 atoms that were outside the box Neighborsearching with a cut-off of 0.48 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48 System total charge: 0.000 Grid: 73 x 73 x 51 cells Successfully made neighbourlist nri = 3007232, nrj = 82473964 Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653 atoms. Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182 atoms. Added 776673 molecules Generated solvent containing 2330019 atoms in 776673 residues Writing generated configuration to outh2o.gro Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1# Go Rough, Oppose Many Angry Chinese Serial killers Output configuration contains 2331459 atoms in 776762 residues Volume : 23276.3 (nm^3) Density: 1001.32 (g/l) Number of SOL molecules: 776673 Processing topology Adding line for 776673 solvent molecules to topology file (topol.top) Later on, I used -d 0.5. I still get around 71 water molecules in the system. Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9 A and 8.4 A respectively. I need to know if I have done something wrong in setting up the system. Is there any way to get feasible number of solvent molecules? Thanks Nikunj -- 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] Large number of solvent molecules
Thank you Dr. Dallas. Yes I think the issue is that the starting conformation is linear, as I want to study its folding properties. I tried the same with helical starting conformation, and got around 11 water molecules, which is still ok. I am trying to find a way to simulate a 89 aa peptide in linear starting conformation such that the simulation is practically feasible. On Tue, May 14, 2013 at 10:45 AM, Dallas Warren dallas.war...@monash.eduwrote: From the box volume printed in the script output it appears you have a box that is approximately a 28nm cube. And that size box requires a significant number of water molecules to fill up, so that number you have in there (~770,000) seems about correct. If you want to have less water molecules, then you will need to make the simulation cell smaller. Whether that is possible or not depends on what you are looking to observe, how big the molecule you are solvating is etc. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - 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 Nikunj Maheshwari Sent: Tuesday, 14 May 2013 3:04 PM To: Discussion list for GROMACS users Subject: [gmx-users] Large number of solvent molecules Dear all, I am trying to see the folding of a 89 aa peptide. So I am setting up the system from linear conformation. I gave the following commands to build the box and add the solvent molecules. editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro Reading solute configuration Go Rough, Oppose Many Angry Chinese Serial killers Containing 1440 atoms in 89 residues Initialising van der waals distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC- MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 18x18x13 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 909792 residues Calculating Overlap... box_margin = 0.315 Removed 324522 atoms that were outside the box Neighborsearching with a cut-off of 0.48 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48 System total charge: 0.000 Grid: 73 x 73 x 51 cells Successfully made neighbourlist nri = 3007232, nrj = 82473964 Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653 atoms. Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182 atoms. Added 776673 molecules Generated solvent containing 2330019 atoms in 776673 residues Writing generated configuration to outh2o.gro Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1# Go Rough, Oppose Many Angry Chinese Serial killers Output configuration contains 2331459 atoms in 776762 residues Volume : 23276.3 (nm^3) Density: 1001.32 (g/l) Number of SOL molecules: 776673 Processing topology Adding line for 776673 solvent molecules to topology file (topol.top) Later on, I used -d 0.5. I still get around 71 water molecules in the system. Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9 A and 8.4 A respectively. I need to know if I have done something wrong in setting up the system. Is there any way to get feasible number of solvent molecules? Thanks Nikunj -- 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
[gmx-users] Error in pdb2gmx
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? Thanks.. -- 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] Maximum protein size for REMD?
I understand the point now. Bigger the system, closer will be the spacing. One thing though: The average energy (mu) returned by the web server for each temperature is 7-8 times more than the actual energy returned after REMD was over. Is there something we are missing here? Thanks. On Tue, Apr 9, 2013 at 6:42 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Thats true with our case as well. The spacing was very small, and we got almost 70 replicas for our protein between 280-410K. That's why, we are thinking of any alternate way of getting the spacing, and started using polynomial fit of the average energies we obtained from our first run. Do you have any thoughts on that? You can space them however you want, but you will only get exchanges if they are close enough in temperature. The spacing returned by the generator is not small because it wants you to use excess compute resources! It needs to be small for big systems. Mark On Tue, Apr 9, 2013 at 2:03 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- 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 -- 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 -- 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 -- 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] doubt in remd
Hi. Glad to know that your REMD was successful. We are trying to do the same, but are stuck in between. Can you tell us, how did you got the temperature spacing? Thanks On Tue, Apr 9, 2013 at 11:59 AM, Shine A shin...@iisertvm.ac.in wrote: Respected sir, I successfully completed REMD simulation. Now I am struggling with analysis part. Here how I select the global minimum from replica? Can you give some suggestions about the analysis part? -- 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
[gmx-users] Maximum protein size for REMD?
Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- 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] Maximum protein size for REMD?
How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- 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 -- 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] Maximum protein size for REMD?
Thats true with our case as well. The spacing was very small, and we got almost 70 replicas for our protein between 280-410K. That's why, we are thinking of any alternate way of getting the spacing, and started using polynomial fit of the average energies we obtained from our first run. Do you have any thoughts on that? On Tue, Apr 9, 2013 at 2:03 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I used the REMD temperature generator. Needless to say, we got really tight spacing and the enhancement to the sampling was probably small. The whole setup was pretty experimental. The run was completed. Erik On 9 Apr 2013, at 10:01, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: How did you get the final temperature spacing for the run? Did you get the fitted values using polynomial fit? Was the run completed? On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I've tried one with 666 aa, but with no publishable results. On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all... Does anyone has any idea what is the maximum protein size for which a successful REMD run has taken place? We have went through lots of research papers, but could not find any protein/peptide above 100 aa related to REMD. We have a protein of 292 aa. Thanks. -- 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 -- 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 -- 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] REMD temperature spacing formula
Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- 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] REMD temperature spacing formula
Thanks for that link. I have used it, but it only takes system size properties. It doesn't take the potential energy values at all. I am looking if someone has used any alternate for temperature spacing generation? On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote: Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, We are stuck at the last stage of running a successful REMD. We have obtained average potential energy by fitting the energy values from initial MD. We want to get the temperature spacing for 72 replicas, starting from 280K. We have gone through numerous papers, but none of them explain clearly how they got the spacing values. Is there any equation/formula/web utility which gives the spacing? Any help will be highly appreciated. Thank you. Nikunj Suhani -- 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 -- 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] Error in REMD
Dear all... We ran REMD simulations for 36 replicas. We got an error which stopped the whole simulation. Reading file md21.tpr, VERSION 4.5.5 (single precision) Loaded with Money Reading file md24.tpr, VERSION 4.5.5 (single precision) Loaded with Money --- Program mdrun_mpi, VERSION 4.5.5 Source code file: symtab.c, line: 108 Fatal error: symtab get_symtab_handle 1031126655 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The World is a Friendly Place (Magnapop) Error on node 35, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 35 out of 36 gcq#103: The World is a Friendly Place (Magnapop) MPI: Global rank 35 is aborting with error code -1. Can someone help us in knowing what the error means and how to it can be rectified? Thanks -- 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] REMD temperature spacing error
I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? 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 -- 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] REMD temperature spacing error
Sorry. I thought it was related to Boltzmann constt. Then how is 'k' calculated ? On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote: k is dimensionless. It does not relate to Boltzmann's constant. The exponential spacing it produces would lead to replica exchange rates that are constant over the T range, under certain assumptions (e.g. papers by David A Kofke). In practice, it normally would not lead to such rates. Whether constant exchange rate is even useful/meaningful is another matter (e.g. papers by Walter Nadler Ulrich Hansmann). Mark On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: I think determining k in the equation is not clear. How is it related to a system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting temperature, the temp. spacing will be the same. Is that correct? On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all. We are trying to run REMD on two proteins : 292 and 44 aa residues using GROMACS 4.6. We are unable to obtain the temperature spacing using REMD temperature generator (http://folding.bmc.uu.se/remd/) as it is giving myriad temperature ranges (in the order of 150 for 250-550K range) Sounds normal for the kind of system you seem to have. Higher numbers of degrees of freedom require closer temperature spacing. Is there any other way to determine the spacing? Can the equation T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? Yes, but if you want exchanges to occur, there are constraints on the size of k. What's so hard about T(i+1)=T(i)*k? 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 -- 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 -- 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
