[gmx-users] residuetype.dat
Dear gmx users, Where can I find residuetypes.dat file? I couldn't find this in gmx forcefied. Thanks in advance. 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
Re: [gmx-users] H-atoms in .hdb file
Thanks for your replies. I found the residuetypes.dat file in top directory of GROMACS package. I need to add the FOR to this file. But it's question for me where am I supposed to set the residuetypes.dat file? In FF folder existed in my working directory? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 8:20 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 11:47 AM, Shima Arasteh wrote: OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it? Dangling bond errors were introduced as part of the output in Gromacs 4.5. The aminoacids.dat file was only used by older (4.0.x and earlier) versions of Gromacs. You need to be modifying residuetypes.dat to indicate that FOR is a Protein residue so that the chain is continuous with respect to its content type. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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 list gmx-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] H-atoms in .hdb file
I added the FOR residue as protein in residuetypes.dat file, but still says it's not identified as protein/DNA/RNA. Would you mind helping me with your suggestions? Thanks in advance Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 8:20 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 11:47 AM, Shima Arasteh wrote: OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it? Dangling bond errors were introduced as part of the output in Gromacs 4.5. The aminoacids.dat file was only used by older (4.0.x and earlier) versions of Gromacs. You need to be modifying residuetypes.dat to indicate that FOR is a Protein residue so that the chain is continuous with respect to its content type. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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 list gmx-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] H-atoms in .hdb file
As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose none as the N-terminus . But after processing the .pdb file the FOR is identified itself but not identified as protein. Any suggestion please? Thanks in advance Sincerely, Shima From: Mark Abraham mark.abra...@anu.edu.au To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Wednesday, June 27, 2012 11:54 AM Subject: Re: [gmx-users] H-atoms in .hdb file On 27/06/12, Shima Arasteh shima_arasteh2...@yahoo.com wrote: I added the FOR residue as protein in residuetypes.dat file, but still says it's not identified as protein/DNA/RNA. Would you mind helping me with your suggestions? Apparently it's not been done right, but we don't have enough detail about what you've done to know what you've done wrong. Look carefully at the contents of the file you changed, and inspect your output carefully for clues. Mark Thanks in advance Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 8:20 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 11:47 AM, Shima Arasteh wrote: OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it? Dangling bond errors were introduced as part of the output in Gromacs 4.5. The aminoacids.dat file was only used by older (4.0.x and earlier) versions of Gromacs. You need to be modifying residuetypes.dat to indicate that FOR is a Protein residue so that the chain is continuous with respect to its content type. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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 list gmx-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 list gmx-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] wrong distances with g_dist
Dear Dmytro Kovalskyy, The ARG CZ is at the end (tip of the ARG), what does the distances look like over time? A floppy long amino acid? And your actual distance calculation? Is it from a graphics/pdb file, or how is it measured? Stephan Original-Nachricht Datum: Tue, 26 Jun 2012 16:14:31 -0500 Von: Dmytro Kovalskyy kovals...@uthscsa.edu An: gmx-users@gromacs.org Betreff: [gmx-users] wrong distances with g_dist Hi, I try to calculate distance between two atoms with g_dist. Somewhat I get distance lower than actual. Here there are coordinates of the two atoms (PDB format) ATOM702 CZ ARG X 45 5.930 9.230 41.740 0.00 0.00 ATOM 2751 CA PHE X 177 41.710 45.000 27.180 0.00 0.00 And the distance I get from g_dist is 4.6260725 nm while the actual is 5.265 nm. What the problem can be? Dmytro -- 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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 using grompp: number of coordinates in coordinate file does not match topology
Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html Bests, Eva -- 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] Fwd: About Justin Lipid-protein simulation tutorial
On 6/27/12 1:23 AM, rama david wrote: Hi Gromacs Friends, I am doing Justin-lipid tutorialer http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html In these the npt.mdp has a parameter refcoord_scaling = com Why these parameter is introduced in NPT of lipid-protein simulation and not use in Lysozyme in water simulation ??? It is used in the lysozyme tutorial. Some time ago, I was informed that the line was missing from the .mdp file, so if you completed the tutorial during that time, the line was missing. grompp should have produced an obvious warning, however. Please give the detail on why to use these parameter?? If the reference coordinates are not scaled, you can get spurious contributions to the virial and pressure. There is some discussion on this (admittedly not much) in the manual. -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] H-atoms in .hdb file
On 6/27/12 3:38 AM, Shima Arasteh wrote: As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose none as the N-terminus . But after processing the .pdb file the FOR is identified itself but not identified as protein. How so? What line did you add to residuetypes.dat, and what was the exact problematic output of pdb2gmx? -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 using grompp: number of coordinates in coordinate file does not match topology
On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -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] H-atoms in .hdb file
I added this line to the residuetypes.dat file: FOR Protein Then running this command: pdb2gmx -f protein.pdb -water spc -ter Written as blow: Processing chain 1 (177 atoms, 25 residues) Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. Identified residue VAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. Asked for terminus: I chose none as the N-terminus. Getting this: Processing chain 1 (177 atoms, 25 residues) Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. Identified residue VAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for VAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus VAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: None 0 End terminus GLY-24: COO- --- Program pdb2gmx, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. Would you helping me with it with your useful suggestions? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 2:58 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/27/12 3:38 AM, Shima Arasteh wrote: As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose none as the N-terminus . But after processing the .pdb file the FOR is identified itself but not identified as protein. How so? What line did you add to residuetypes.dat, and what was the exact problematic output of pdb2gmx? -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
Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial
Thank you Justin for your Explaination Please Would you me the Reason Why these parameter is present in Equilibration mdp and not in production run mdp file ( for both lysozyme and lipid simulation ) With Best Wishes and regardsRama -- 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] Fwd: About Justin Lipid-protein simulation tutorial
On 6/27/12 7:01 AM, rama david wrote: Thank you Justin for your Explaination Please Would you me the Reason Why these parameter is present in Equilibration mdp and not in production run mdp file ( for both lysozyme and lipid simulation ) It is only relevant when applying position restraints. -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] Fwd: About Justin Lipid-protein simulation tutorial
Thank you Justin, But you not added these parameter to the Umbrella sampling NPT file. Is any reason not to use these parameter in Umbrella sampling?? I run the simulation of peptide withought any refcoord_scaling = com in mdp file and now is it will affect result significantly?? Is it wrong simulation??? How to check these parameter affect my result sensitivity??? Please give me valuable guidance to solve my query.. With Best Wishes and regards, Rama David -- 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] Fwd: About Justin Lipid-protein simulation tutorial
On 6/27/12 7:16 AM, rama david wrote: Thank you Justin, But you not added these parameter to the Umbrella sampling NPT file. Is any reason not to use these parameter in Umbrella sampling?? If it is missing, it's a simple typographical omission. I have adapted these tutorials over many years and occasionally something like this slips through the cracks. Hence why it's always important to pay attention to the warnings grompp prints out. I run the simulation of peptide withought any refcoord_scaling = com in mdp file and now is it will affect result significantly?? Is it wrong simulation??? How to check these parameter affect my result sensitivity??? The pressure might be slightly off. -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] H-atoms in .hdb file
On 6/27/12 6:38 AM, Shima Arasteh wrote: I added this line to the residuetypes.dat file: FOR Protein Then running this command: pdb2gmx -f protein.pdb -water spc -ter Written as blow: Processing chain 1 (177 atoms, 25 residues) Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. Identified residue VAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. Asked for terminus: I chose none as the N-terminus. Getting this: Processing chain 1 (177 atoms, 25 residues) Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. Identified residue VAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for VAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus VAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: None 0 End terminus GLY-24: COO- --- Program pdb2gmx, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. Would you helping me with it with your useful suggestions? I honestly have no idea why that's not working. It's the exact same workflow used with all other capping groups and I use it routinely. -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
[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp
Dear Gromacs Users, I am using gromacs version 4.5.5. , while running grompp (for any purpose i.e. minimization , equilibration etc. ) I am getting following screen output without any warning, error or note relevant to it. Generated 830 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'Protein_B' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' My question is whether to ignore or consider this as an error ? I really don't know why this screen output is coming which I never faced ? Is there any mistake by me ? Please suggest . cg.mdp for reference ; Conjugate Minimization ; Protein - Water - Ligand ( all free to move) ; ; ; Title = Pro-Lig H2O define = -DFLEXIBLE ; specifies flexible water constraints = none integrator = cg nsteps = 2000 ns_type = grid rlist = 1.2 coulombtype = pme vdw-type = cut-off rvdw = 1.2 rcoulomb = 1.2 ; ; Energy Minimization Stuff ; ; emtol = 0.001 emstep = 0.01 Thanking you in advance . Regards, Pavan Payghan -- 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] About Exclusion of bonded and non bonded parameters while running grompp
On 6/27/12 7:36 AM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am using gromacs version 4.5.5. , while running grompp (for any purpose i.e. minimization , equilibration etc. ) I am getting following screen output without any warning, error or note relevant to it. Generated 830 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'Protein_B' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' My question is whether to ignore or consider this as an error ? This output is perfectly normal, and is (or at least, should be) present for any system that has more than monoatomic species. I really don't know why this screen output is coming which I never faced ? Is there any mistake by me ? Please suggest . There is no mistake. Please refer to the manual, section 4.6.1. -Justin cg.mdp for reference ; Conjugate Minimization ; Protein - Water - Ligand ( all free to move) ; ; ; Title = Pro-Lig H2O define = -DFLEXIBLE ; specifies flexible water constraints = none integrator = cg nsteps = 2000 ns_type = grid rlist = 1.2 coulombtype = pme vdw-type = cut-off rvdw = 1.2 rcoulomb = 1.2 ; ; Energy Minimization Stuff ; ; emtol = 0.001 emstep = 0.01 Thanking you in advance . Regards, Pavan Payghan -- 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
[gmx-users] Pulling ligand - Different Profiles (Force vs time)
Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling : grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstfout = 500 nstxtcout = 1000 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.2 vdwtype = Switch rvdw-switch = 1.0 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 I run 3 pulling simulations with the same mdp and I obtain 3 different profiles (Force vs time). Then I used 2xlonger pulling with the same pulling distance and I run 3 simulations again. Each time I obtain different profile. Can anyone explain me this? I am using velocities from npt simulation as above (gen_vel = no and continuation = yes) so I presume the output should be similar. Please, advice. Steven -- 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] Atoms get frozen with Nose Hoover thermostat with Parrinello-Rahman barostat for a system of an ion of charge +2 in flexible water molecules
On 27/06/12 05:20, Surya Prakash Tiwari wrote: Dear Gromacs users, I am having a very strange problem with Nose Hoover thermostat with Parrinello-Rahman barostat NPT simulations for a system of an ion of charge +2 in flexible water molecules. Flexible water is taken from J. Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877. The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25. Atoms very soon get frozen after the simulation starts and they remain frozen, they do not move at all. Only simulation box oscillates, which causes atoms to oscillate little bit but they do not move at all. To me it looks like a case of this artefact: http://en.wikipedia.org/wiki/Flying_ice_cube but I don't know exactly what is causing it in your system. Perhaps the article can help you triage... -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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 using grompp: number of coordinates in coordinate file does not match topology
Hi Justin, thank you for your answer. Now it worked and I could do the minimization. But now I have the same problem again but now the difference is 630. So what I did is that I ran the minimization and everything worked. And than I used the perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat command of the tutorial and now I got the error: number of coordinates in coordinate file (system_shrink1.gro, 9220) does not match topology (topol.top, 9850) But I changed nothing at the topology file. Bests, Eva On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -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 -- 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 using grompp: number of coordinates in coordinate file does not match topology
Got it already. Thank you!! On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800) I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Pulling ligand - Different Profiles (Force vs time)
On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling : grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50; 1 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstfout = 500 nstxtcout = 1000 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.2 vdwtype = Switch rvdw-switch = 1.0 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 I run 3 pulling simulations with the same mdp and I obtain 3 different profiles (Force vs time). Then I used 2xlonger pulling with the same pulling distance and I run 3 simulations again. Each time I obtain different profile. Can anyone explain me this? I am using velocities from npt simulation as above (gen_vel = no and continuation = yes) so I presume the output should be similar. Please, advice. I assume you're passing a checkpoint file to grompp? If you're relying on velocities from the .gro file, they are of insufficient precision to guarantee proper continuation. Small variations are inherent in any simulation set, and in the case of pulling, small changes (though intentional) are the basis for Jarzynski's method. In any case, all MD simulations are chaotic and so it depends on what your definition of different is in the context of whether or not there are meaningful changes imparted through the course of each simulation. Also note that in the absence of the -reprod flag, the same .tpr file may result in a slightly different outcome. The implications of these outcomes are limited by sampling; the ensemble should converge with sufficient time and/or replicates. For non-equilibrium processes like pulling, convergence is probably harder, but again you have to ask whether the differences are meaningful. http://www.gromacs.org/Documentation/Terminology/Reproducibility -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 * Only plain text messages are allowed! * 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] Pulling ligand - Different Profiles (Force vs time)
On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling : grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstfout = 500 nstxtcout = 1000 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.2 vdwtype = Switch rvdw-switch = 1.0 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 I run 3 pulling simulations with the same mdp and I obtain 3 different profiles (Force vs time). Then I used 2xlonger pulling with the same pulling distance and I run 3 simulations again. Each time I obtain different profile. Can anyone explain me this? I am using velocities from npt simulation as above (gen_vel = no and continuation = yes) so I presume the output should be similar. Please, advice. I assume you're passing a checkpoint file to grompp? If you're relying on velocities from the .gro file, they are of insufficient precision to guarantee proper continuation. Thank you Justin. I am using according to your tutorial: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull Would you suggest: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ?? Profiles do not vary slightly - the maximum pulling force (breaking point) varies from 290 to 500 kJ/mol nm2 which is really a lot. Steven Small variations are inherent in any simulation set, and in the case of pulling, small changes (though intentional) are the basis for Jarzynski's method. In any case, all MD simulations are chaotic and so it depends on what your definition of different is in the context of whether or not there are meaningful changes imparted through the course of each simulation. Also note that in the absence of the -reprod flag, the same .tpr file may result in a slightly different outcome. The implications of these outcomes are limited by sampling; the ensemble should converge with sufficient time and/or replicates. For non-equilibrium processes like pulling, convergence is probably harder, but again you have to ask whether the differences are meaningful. http://www.gromacs.org/Documentation/Terminology/Reproducibility -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)
On 6/27/12 9:36 AM, Steven Neumann wrote: On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling : grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50; 1 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstfout = 500 nstxtcout = 1000 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.2 vdwtype = Switch rvdw-switch = 1.0 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 I run 3 pulling simulations with the same mdp and I obtain 3 different profiles (Force vs time). Then I used 2xlonger pulling with the same pulling distance and I run 3 simulations again. Each time I obtain different profile. Can anyone explain me this? I am using velocities from npt simulation as above (gen_vel = no and continuation = yes) so I presume the output should be similar. Please, advice. I assume you're passing a checkpoint file to grompp? If you're relying on velocities from the .gro file, they are of insufficient precision to guarantee proper continuation. Thank you Justin. I am using according to your tutorial: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull Would you suggest: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ?? No, I would not, especially if the NPT run uses position restraints, in which case the two phases are different. I missed the command line in the earlier message. What you are doing makes sense. Profiles do not vary slightly - the maximum pulling force (breaking point) varies from 290 to 500 kJ/mol nm2 which is really a lot. Consult the points below and watch your trajectories. If you're getting different forces, your ligands are experiencing different interactions. SMD is a path-dependent, non-equilibrium process. Good sampling and a justifiable path are key. -Justin Small variations are inherent in any simulation set, and in the case of pulling, small changes (though intentional) are the basis for Jarzynski's method. In any case, all MD simulations are chaotic and so it depends on what your definition of different is in the context of whether or not there are meaningful changes imparted through the course of each simulation. Also note that in the absence of the -reprod flag, the same .tpr file may result in a slightly different outcome. The implications of these outcomes are limited by sampling; the ensemble should converge with sufficient time and/or replicates. For non-equilibrium processes like pulling, convergence is probably harder, but again you have to ask whether the differences are meaningful. http://www.gromacs.org/Documentation/Terminology/Reproducibility -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
Re: [gmx-users] H-atoms in .hdb file
Anyway, thanks for your reply . I appreciate you. Sincerely, Shima Sincerely, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, June 27, 2012 3:54 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/27/12 6:38 AM, Shima Arasteh wrote: I added this line to the residuetypes.dat file: FOR Protein Then running this command: pdb2gmx -f protein.pdb -water spc -ter Written as blow: Processing chain 1 (177 atoms, 25 residues) Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. Identified residue VAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. Asked for terminus: I chose none as the N-terminus. Getting this: Processing chain 1 (177 atoms, 25 residues) Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA. Identified residue VAL1 as a starting terminus. Identified residue GLY24 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for VAL-1 0: NH3+ 1: NH2 2: None 2 Start terminus VAL-1: None Select end terminus type for GLY-24 0: COO- 1: COOH 2: None 0 End terminus GLY-24: COO- --- Program pdb2gmx, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. Would you helping me with it with your useful suggestions? I honestly have no idea why that's not working. It's the exact same workflow used with all other capping groups and I use it routinely. -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 list gmx-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 * Only plain text messages are allowed! * 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] Pulling ligand - Different Profiles (Force vs time)
Thank you Justin. On Wed, Jun 27, 2012 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 9:36 AM, Steven Neumann wrote: On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/27/12 7:48 AM, Steven Neumann wrote: Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling : grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstfout = 500 nstxtcout = 1000 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.2 vdwtype = Switch rvdw-switch = 1.0 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 I run 3 pulling simulations with the same mdp and I obtain 3 different profiles (Force vs time). Then I used 2xlonger pulling with the same pulling distance and I run 3 simulations again. Each time I obtain different profile. Can anyone explain me this? I am using velocities from npt simulation as above (gen_vel = no and continuation = yes) so I presume the output should be similar. Please, advice. I assume you're passing a checkpoint file to grompp? If you're relying on velocities from the .gro file, they are of insufficient precision to guarantee proper continuation. Thank you Justin. I am using according to your tutorial: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull Would you suggest: grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ?? No, I would not, especially if the NPT run uses position restraints, in which case the two phases are different. I missed the command line in the earlier message. What you are doing makes sense. Profiles do not vary slightly - the maximum pulling force (breaking point) varies from 290 to 500 kJ/mol nm2 which is really a lot. Consult the points below and watch your trajectories. If you're getting different forces, your ligands are experiencing different interactions. SMD is a path-dependent, non-equilibrium process. Good sampling and a justifiable path are key. -Justin Small variations are inherent in any simulation set, and in the case of pulling, small changes (though intentional) are the basis for Jarzynski's method. In any case, all MD simulations are chaotic and so it depends on what your definition of different is in the context of whether or not there are meaningful changes imparted through the course of each simulation. Also note that in the absence of the -reprod flag, the same .tpr file may result in a slightly different outcome. The implications of these outcomes are limited by sampling; the ensemble should converge with sufficient time and/or replicates. For non-equilibrium processes like pulling, convergence is probably harder, but again you have to ask whether the differences are meaningful. http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin --
[gmx-users] make index
Hi everybody, I want to make an index with make_ndx. But when I just wanted to group SOL and CL and Protein and DPPC it tells me when I want to run grompp afterwards that there are some residues not indexed. I thought that that might be because the NA-ions are not grouped. But when I want to group them together with the SOL and the CL with the command 14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could not be found. That is reasonable since my group is called: NA_CL_SOL So my question is: how can I rename such a index group? Bests, Eva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] make index
On 6/27/12 11:08 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to make an index with make_ndx. But when I just wanted to group SOL and CL and Protein and DPPC it tells me when I want to run grompp afterwards that there are some residues not indexed. Copying and pasting an error message is much more effective. I could guess at what this error is, but seeing it would be more useful. I thought that that might be because the NA-ions are not grouped. But when I want to group them together with the SOL and the CL with the command 14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could not be found. That is reasonable since my group is called: NA_CL_SOL So my question is: how can I rename such a index group? The names specified in the .mdp file and .ndx files must match, so you can either change the names in the .mdp file (easiest), use a text editor to modify the name of the group in the .ndx file (same principle, probably a little more scrolling and/or find and replace), or use make_ndx to rename the groups (not very efficient in this case). -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 * Only plain text messages are allowed! * 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] pdb2gmx error
Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OG OA -0.548 2 HG HO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: pdb2gmx error
You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OG OA -0.548 2 HG HO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 12:25 PM, Shima Arasteh wrote: You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with MISSING entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OGOA -0.548 2 HGHO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing listgmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- 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 * Only plain text messages are allowed! * 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] tabulated potentials and soft core free energy - this should not work ....
Hi, i meant to perform a free energy calculation to get the chemical potential of water, and made a number of input files based on the excellent tutorial by Justin Lemkul. (Without thinking) I also tried using a tabulated potential for electrostatics with: coulombtype = User but it seems to work - all the numbers in dhdl.xvg are finite and non-zero, and neither mdrun nor grompp give me a warning) but then it shouldn't work ... how is Gromacs supposed to calculate the dU/dlambda term ? or Is this calculated numerically? or did i overlook something here? below my mdp file thanks for any advice! michael mdp: integrator = sd nsteps = 10 dt = 0.002 ; pbc = xyz nstcomm = 100 comm_grps = System ; nstxtcout = 0 nstenergy = 100 nst_log = 0 nstxout = 0 nstvout = 0 ; rlist = 1.35 ; coulombtype = User rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 ; tc_grps = system tau_t = 1.0 ref_t = 300 ; Pcoupl = Berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic ; constraints = hbonds lincs_iter = 8 ; free_energy = yes init_lambda = 0.50 delta_lambda = 0 foreign_lambda = 0.40 0.60 dhdl_derivatives = yes sc_alpha = 0.5 sc_power = 1 sc_sigma = 0.5 nstdhdl = 100 couple-moltype = w1 couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no === Why be happy when you could be normal? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: pdb2gmx error
I know that no missing atom is here. As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement. Please help me, I don't know what to do :( Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:25 PM, Shima Arasteh wrote: You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with MISSING entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OG OA -0.548 2 HG HO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 12:43 PM, Shima Arasteh wrote: I know that no missing atom is here. As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement. Please help me, I don't know what to do :( Please copy and paste the entirety of the first three residues in your .pdb file so we can see what you're working with. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:25 PM, Shima Arasteh wrote: You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with MISSING entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OGOA -0.548 2 HGHO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing listgmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
OK. PDB FILE IS AS BELOW: HETATM 1 C FOR 0 -0.721 1.600 1.249 HETATM 2 O FOR 0 -0.839 2.806 1.453 ATOM 3 N VAL 1 -1.227 0.728 2.125 ATOM 4 CA VAL 1 -1.918 1.159 3.323 ATOM 5 C VAL 1 -1.969 2.678 3.410 ATOM 6 O VAL 1 -0.931 3.335 3.447 ATOM 7 CB VAL 1 -1.219 0.644 4.576 ATOM 8 CG1 VAL 1 0.208 1.178 4.618 ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 CB SER 2 -4.138 5.196 2.320 ATOM 13 OG SER 2 -4.296 6.612 2.437 ATOM 14 C SER 2 -4.135 5.054 4.778 ATOM 15 O SER 2 -5.272 4.628 4.966 Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 9:14 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:43 PM, Shima Arasteh wrote: I know that no missing atom is here. As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement. Please help me, I don't know what to do :( Please copy and paste the entirety of the first three residues in your .pdb file so we can see what you're working with. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:25 PM, Shima Arasteh wrote: You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with MISSING entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OG OA -0.548 2 HG HO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- 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 list
[gmx-users] Re: pdb2gmx error
Hi, removing the HETATMs worked for me when i used AMBER99SB's rtp file. What force field are you using? Have you added the FOR topology manually (I know this is besides the point about the problem with serine) AMBER99SB seemed to only have topology for acetate [ACE] I am also learning through this. Sincerely, Shounak Shima Arasteh wrote OK. PDB FILE IS AS BELOW: HETATM 1 C FOR 0 -0.721 1.600 1.249 HETATM 2 O FOR 0 -0.839 2.806 1.453 ATOM 3 N VAL 1 -1.227 0.728 2.125 ATOM 4 CA VAL 1 -1.918 1.159 3.323 ATOM 5 C VAL 1 -1.969 2.678 3.410 ATOM 6 O VAL 1 -0.931 3.335 3.447 ATOM 7 CB VAL 1 -1.219 0.644 4.576 ATOM 8 CG1 VAL 1 0.208 1.178 4.618 ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 CB SER 2 -4.138 5.196 2.320 ATOM 13 OG SER 2 -4.296 6.612 2.437 ATOM 14 C SER 2 -4.135 5.054 4.778 ATOM 15 O SER 2 -5.272 4.628 4.966 Sincerely, Shima - Original Message - From: Justin A. Lemkul lt;jalemkul@gt; To: Discussion list for GROMACS users lt;gmx-users@gt; Cc: Sent: Wednesday, June 27, 2012 9:14 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:43 PM, Shima Arasteh wrote: I know that no missing atom is here. As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement. Please help me, I don't know what to do :( Please copy and paste the entirety of the first three residues in your .pdb file so we can see what you're working with. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul lt;jalemkul@gt; To: Shima Arasteh lt;shima_arasteh2001@gt;; Discussion list for GROMACS users lt;gmx-users@gt; Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:25 PM, Shima Arasteh wrote: You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with MISSING entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin Sincerely, Shima - Original Message - From: shounakb lt;baners4@gt; To: gmx-users@ Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OG OA -0.548 2 HG HO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read
Re: [gmx-users] Re: pdb2gmx error
If I remove HETATMs, then what about the FOR residue? Thanks for your suggestions. Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 9:42 PM Subject: [gmx-users] Re: pdb2gmx error Hi, removing the HETATMs worked for me when i used AMBER99SB's rtp file. What force field are you using? Have you added the FOR topology manually (I know this is besides the point about the problem with serine) AMBER99SB seemed to only have topology for acetate [ACE] I am also learning through this. Sincerely, Shounak Shima Arasteh wrote OK. PDB FILE IS AS BELOW: HETATM 1 C FOR 0 -0.721 1.600 1.249 HETATM 2 O FOR 0 -0.839 2.806 1.453 ATOM 3 N VAL 1 -1.227 0.728 2.125 ATOM 4 CA VAL 1 -1.918 1.159 3.323 ATOM 5 C VAL 1 -1.969 2.678 3.410 ATOM 6 O VAL 1 -0.931 3.335 3.447 ATOM 7 CB VAL 1 -1.219 0.644 4.576 ATOM 8 CG1 VAL 1 0.208 1.178 4.618 ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 CB SER 2 -4.138 5.196 2.320 ATOM 13 OG SER 2 -4.296 6.612 2.437 ATOM 14 C SER 2 -4.135 5.054 4.778 ATOM 15 O SER 2 -5.272 4.628 4.966 Sincerely, Shima - Original Message - From: Justin A. Lemkul lt;jalemkul@gt; To: Discussion list for GROMACS users lt;gmx-users@gt; Cc: Sent: Wednesday, June 27, 2012 9:14 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:43 PM, Shima Arasteh wrote: I know that no missing atom is here. As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement. Please help me, I don't know what to do :( Please copy and paste the entirety of the first three residues in your .pdb file so we can see what you're working with. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul lt;jalemkul@gt; To: Shima Arasteh lt;shima_arasteh2001@gt;; Discussion list for GROMACS users lt;gmx-users@gt; Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:25 PM, Shima Arasteh wrote: You mean the order of C and O should be changed in .pdb file? If yes, it didn't work! The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with MISSING entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin Sincerely, Shima - Original Message - From: shounakb lt;baners4@gt; To: gmx-users@ Cc: Sent: Wednesday, June 27, 2012 8:39 PM Subject: [gmx-users] Re: pdb2gmx error Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote Hi all, I got this error : Atom CA is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 2. I checked the pdb file and rtp file. .rtp file: [ SER ] [ atoms ] N N -0.280 0 H H 0.280 0 CA CH1 0.000 1 CB CH2 0.150 2 OG OA -0.548 2 HG HO 0.398 2 C C 0.380 3 O O -0.380 3 .pdb file: ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 C SER 2 -4.135 5.054 4.778 ATOM 13 O SER 2 -5.272 4.628 4.966 ATOM 14 CB SER 2 -4.138 5.196 2.320 ATOM 15 OG SER 2 -4.296 6.612 2.437 I guess they are in agreement, so what's the problem? Sincerely, Shima -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text
Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 12:50 PM, Shima Arasteh wrote: OK. PDB FILE IS AS BELOW: HETATM1 C FOR 0 -0.721 1.600 1.249 HETATM2 O FOR 0 -0.839 2.806 1.453 ATOM 3 N VAL 1 -1.227 0.728 2.125 ATOM 4 CA VAL 1 -1.918 1.159 3.323 ATOM 5 C VAL 1 -1.969 2.678 3.410 ATOM 6 O VAL 1 -0.931 3.335 3.447 ATOM 7 CB VAL 1 -1.219 0.644 4.576 ATOM 8 CG1 VAL 1 0.208 1.178 4.618 ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 CB SER 2 -4.138 5.196 2.320 ATOM 13 OG SER 2 -4.296 6.612 2.437 ATOM 14 C SER 2 -4.135 5.054 4.778 ATOM 15 O SER 2 -5.272 4.628 4.966 The error comes from the VAL residue (residue 2 in the sequence based on the internal numbering used by pdb2gmx, as I suspected earlier). Note the following line in the [impropers] section of aminoacids.rtp in the [VAL] entry: -C -CA N-O The improper is defined using the position of a CA atom in the preceding residue, which in this case does not exist because it is not a normal amino acid (though an ACE cap will also work because its atoms are named suitably). This method of defining the improper is somewhat odd. Using a more modern force field like Gromos96 53a6 does not give rise to this error, as all impropers are defined using only -C or +N. Just another reason to use a non-deprecated force field :) -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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
I know it's much better to use a non-deprecated ff. But what could I do? I have to regenerate the results of simulation done by gmx.ff . Aren't there any solution to pass this step? I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :) Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 9:55 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:50 PM, Shima Arasteh wrote: OK. PDB FILE IS AS BELOW: HETATM 1 C FOR 0 -0.721 1.600 1.249 HETATM 2 O FOR 0 -0.839 2.806 1.453 ATOM 3 N VAL 1 -1.227 0.728 2.125 ATOM 4 CA VAL 1 -1.918 1.159 3.323 ATOM 5 C VAL 1 -1.969 2.678 3.410 ATOM 6 O VAL 1 -0.931 3.335 3.447 ATOM 7 CB VAL 1 -1.219 0.644 4.576 ATOM 8 CG1 VAL 1 0.208 1.178 4.618 ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 CB SER 2 -4.138 5.196 2.320 ATOM 13 OG SER 2 -4.296 6.612 2.437 ATOM 14 C SER 2 -4.135 5.054 4.778 ATOM 15 O SER 2 -5.272 4.628 4.966 The error comes from the VAL residue (residue 2 in the sequence based on the internal numbering used by pdb2gmx, as I suspected earlier). Note the following line in the [impropers] section of aminoacids.rtp in the [VAL] entry: -C -CA N -O The improper is defined using the position of a CA atom in the preceding residue, which in this case does not exist because it is not a normal amino acid (though an ACE cap will also work because its atoms are named suitably). This method of defining the improper is somewhat odd. Using a more modern force field like Gromos96 53a6 does not give rise to this error, as all impropers are defined using only -C or +N. Just another reason to use a non-deprecated force field :) -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 1:35 PM, Shima Arasteh wrote: I know it's much better to use a non-deprecated ff. But what could I do? I have to regenerate the results of simulation done by gmx.ff . Aren't there any solution to pass this step? I have no idea how to make gmx.ff work. I solved the issue by commenting out the line and seeing that no error resulted. This, of course, isn't an actual solution, just a debugging method. The force field defines its impropers in an odd way, and as such I don't know that there is a workaround. I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :) The sooner, the better. This is an ancient force field, and vastly better parameter sets exist. -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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
Dear Justin, Again, I appreciate you. I learn much from you, feeling happy :) Thanks a lot. Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:10 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:35 PM, Shima Arasteh wrote: I know it's much better to use a non-deprecated ff. But what could I do? I have to regenerate the results of simulation done by gmx.ff . Aren't there any solution to pass this step? I have no idea how to make gmx.ff work. I solved the issue by commenting out the line and seeing that no error resulted. This, of course, isn't an actual solution, just a debugging method. The force field defines its impropers in an odd way, and as such I don't know that there is a workaround. I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS POSSIBLE :) The sooner, the better. This is an ancient force field, and vastly better parameter sets exist. -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Sincerely, Shounak -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998861.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: pdb2gmx error
Dear Shounak, So what's about the FOR residue? I can't eliminate it. I guess if I do as you suggest, I need to add the FOR to n.tdb and then the procedure would be different! Yes, I added the FOR to rtp file on my own. Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:22 PM Subject: [gmx-users] Re: pdb2gmx error Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Sincerely, Shounak -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998861.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 1:58 PM, Shima Arasteh wrote: Dear Shounak, So what's about the FOR residue? I can't eliminate it. I guess if I do as you suggest, I need to add the FOR to n.tdb and then the procedure would be different! You do not need to add FOR to a .tdb entry. These directives are only to modify protonation states of amines and carboxylates. I believe you tried this before, and my comment was that such a procedure would not work (and it didn't). -Justin Yes, I added the FOR to rtp file on my own. Sincerely, Shima - Original Message - From: shounakb bane...@rpi.edu To: gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:22 PM Subject: [gmx-users] Re: pdb2gmx error Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Sincerely, Shounak -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998861.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
:)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 2:05 PM, Shima Arasteh wrote: :)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? The decision should not be whether or not there is an N-formylation on your protein. It seems obvious that you need it. The real issue is how it is represented, which entails two issues: 1. A parent force field to use 2. Parameterization of the formyl group under the rules of the parent force field The mechanics within Gromacs are irrelevant to these concerns and only matter once those points are satisfied. No matter the force field you choose, the assembly of the topology through pdb2gmx is the same. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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 * Only plain text messages are allowed! * 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 -- 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
So as you said it doesn't matter to remove the FOR residue. But I can't understand why the representation of FOR is still required! And, you suggest me to use another forcefield to produce the topology and then go on whit it by gmx ? Would I need to maintain the FOR in the new FF or eliminate it? Honestly I'm a little confused here. Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 2:05 PM, Shima Arasteh wrote: :)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? The decision should not be whether or not there is an N-formylation on your protein. It seems obvious that you need it. The real issue is how it is represented, which entails two issues: 1. A parent force field to use 2. Parameterization of the formyl group under the rules of the parent force field The mechanics within Gromacs are irrelevant to these concerns and only matter once those points are satisfied. No matter the force field you choose, the assembly of the topology through pdb2gmx is the same. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 2:23 PM, Shima Arasteh wrote: So as you said it doesn't matter to remove the FOR residue. But I can't understand why the representation of FOR is still required! I did not say that. Your last message gave the reason why the formyl group is necessary. Have I misunderstood? This is all getting really confusing. If you're adding a formyl cap, then you'd better have a reason for it, otherwise all of this is a grand waste of time. And, you suggest me to use another forcefield to produce the topology and then go on whit it by gmx ? Would I need to maintain the FOR in the new FF or eliminate it? Honestly I'm a little confused here. Yes, you should use a more reliable force field. You should choose it based on significant reading about the pros and cons of different force fields and what people generally use to simulate similar systems. You will then need to re-derive parameters for the formyl group based on the parameterization methodology required by the force field. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 2:05 PM, Shima Arasteh wrote: :)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? The decision should not be whether or not there is an N-formylation on your protein. It seems obvious that you need it. The real issue is how it is represented, which entails two issues: 1. A parent force field to use 2. Parameterization of the formyl group under the rules of the parent force field The mechanics within Gromacs are irrelevant to these concerns and only matter once those points are satisfied. No matter the force field you choose, the assembly of the topology through pdb2gmx is the same. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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 * Only plain text messages are allowed! * 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 -- 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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
You are right. OK, the reason of adding FOR is what I explained a few minutes ago. All over, I'm supposed to use a modern FF . ( In similar researches I found CHARMM is suitable, so I would add FOR as the procedure explained in GROMACS.ORG) For now, because I wanna regenerate an old simulation, I keep the FOR, then here it's stopped! Seeking for a solution! If any suggestion, I look forward hearing from you. THANKS FOR ALL YOUR KIND REPLIES! :) Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 2:23 PM, Shima Arasteh wrote: So as you said it doesn't matter to remove the FOR residue. But I can't understand why the representation of FOR is still required! I did not say that. Your last message gave the reason why the formyl group is necessary. Have I misunderstood? This is all getting really confusing. If you're adding a formyl cap, then you'd better have a reason for it, otherwise all of this is a grand waste of time. And, you suggest me to use another forcefield to produce the topology and then go on whit it by gmx ? Would I need to maintain the FOR in the new FF or eliminate it? Honestly I'm a little confused here. Yes, you should use a more reliable force field. You should choose it based on significant reading about the pros and cons of different force fields and what people generally use to simulate similar systems. You will then need to re-derive parameters for the formyl group based on the parameterization methodology required by the force field. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 2:05 PM, Shima Arasteh wrote: :)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? The decision should not be whether or not there is an N-formylation on your protein. It seems obvious that you need it. The real issue is how it is represented, which entails two issues: 1. A parent force field to use 2. Parameterization of the formyl group under the rules of the parent force field The mechanics within Gromacs are irrelevant to these concerns and only matter once those points are satisfied. No matter the force field you choose, the assembly of the topology through pdb2gmx is the same. -Justin Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- 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 list
[gmx-users] Re: pdb2gmx error
Hi Shima, i do not think pdb2gmx uses the tdb files. However, I feel that the FOR tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb I saw your other thread where you have described the FOR topology you added. I think the atoms should be CA and O and their respective atom types, CH1/CH2 and O. I guess you already have partial charges for the atoms? Shouldn't that solve the problem with VAL that Justin highlighted, without having to comment out the impropers line? Regards, Shounak Shima Arasteh wrote :)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? Sincerely, Shima - Original Message - From: Justin A. Lemkul lt;jalemkul@gt; To: Discussion list for GROMACS users lt;gmx-users@gt; Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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 list gmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998870.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: pdb2gmx error
On 6/27/12 2:42 PM, Shima Arasteh wrote: You are right. OK, the reason of adding FOR is what I explained a few minutes ago. All over, I'm supposed to use a modern FF . ( In similar researches I found CHARMM is suitable, so I would add FOR as the procedure explained in GROMACS.ORG) This sounds like a good idea. For now, because I wanna regenerate an old simulation, I keep the FOR, then here it's stopped! Seeking for a solution! There is one possible solution that I just thought of. Rather than using FOR as its own residue, create a formylated valine, thus eliminating the problem with the call to CA of the preceding residue. The .rtp entry: [ FVAL ] [ atoms ] CN CH1 0.380 0 ON O -0.380 0 N N -0.280 1 H H 0.280 1 CA CH1 0.000 2 CB CH1 0.000 3 CG1 CH3 0.000 4 CG2 CH3 0.000 5 C C 0.380 6 O O -0.380 6 [ bonds ] CNON CN N N H NCA CA C C O CACB CB CG1 CB CG2 [ impropers ] NCNCA H CN -CA NON CA N CCB CB CG2 CG1CA The .hdb entry: FVAL1 1 1 H N CN CA Then add FVAL to residuetypes.dat as a protein residue. Processing the .pdb file you posted before (merging FOR and VAL into FVAL and adjusting names according to the .rtp entry above) works correctly. Disclaimer: this method works (i.e. produces a topology) but I do not necessarily endorse the use of the parameters shown. -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 * Only plain text messages are allowed! * 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] NVT, NPT and then pulling?
Dear Gmx Users, I am wondering whether would you advise to run NVT, NPT (position restrained) and before the pulling simulation e.g of the ligand from protein-ligand complex? As I saw in Justin tutorial he equilibrate the system with only NPT ensemble before pulling. Is that really sufficent e.g. for 200 ps? Thanks, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] NVT, NPT and then pulling?
On 6/27/12 4:30 PM, Steven Neumann wrote: Dear Gmx Users, I am wondering whether would you advise to run NVT, NPT (position restrained) and before the pulling simulation e.g of the ligand from protein-ligand complex? As I saw in Justin tutorial he equilibrate the system with only NPT ensemble before pulling. Is that really sufficent e.g. for 200 ps? There is no catch-all equilibration scheme that works universally. NVT and NPT are commonly run in sequence. My systems in the tutorial are quite robust and a single NPT phase is sufficient. Please do not assume that this is universally true. Your protocol should be based on how stable your systems are and how well your desired observables converge, but that much is true of every simulation. -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 * Only plain text messages are allowed! * 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] Re: pdb2gmx error
sorry about the previous post! I have not yet looked at the code for pdb2gmx (and a lot of other stuff). I think the formyl-valine idea is pretty cool and found this thread very informative. Thank you! Shounak Justin A. Lemkul wrote On 6/27/12 2:49 PM, shounakb wrote: Hi Shima, i do not think pdb2gmx uses the tdb files. However, I feel that the FOR tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb Both of these assertions are incorrect. The *only* Gromacs program that uses .tdb files is pdb2gmx. The FOR cap is on the N-terminus, so it cannot be in .c.tdb. Both .tdb files are irrelevant for this problem, as stated before. I saw your other thread where you have described the FOR topology you added. I think the atoms should be CA and O and their respective atom types, CH1/CH2 and O. This does not solve the problem. If one changes the C atom name to CA then pdb2gmx will certainly complain that the atom C is missing, since improper construction for VAL is dependent upon atoms C and CA being present in the preceding residue. I guess you already have partial charges for the atoms? Shouldn't that solve the problem with VAL that Justin highlighted, without having to comment out the impropers line? Partial charges are irrelevant here. The error complains about an atom not being found, not the charge on any given atom. Shima has a functional .rtp entry for the FOR residue. It is not the problem, VAL is. Better stated, the mechanism used by gmx.ff to generate impropers in this case blocks the use of FOR as a separate residue, since it does not contain the same atoms as an amino acid, specifically a C and CA. -Justin Regards, Shounak Shima Arasteh wrote :)) I can't eliminate it, I decided to do , but when I studied about the structure of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and the reason of this formation is the existence of formyl residues in N-teminals) . Then I got regretful to remove it. Don't you agree? Sincerely, Shima - Original Message - From: Justin A. Lemkul lt;jalemkul@gt; To: Discussion list for GROMACS users lt;gmx-users@gt; Cc: Sent: Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 1:52 PM, shounakb wrote: Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Please see the previous posts on these topics, including the post from just a few minutes ago where I discovered the source of the problem. The FOR residue issue has been an ongoing discussion over several weeks. I will maintain that I do not necessarily believe that a two-atom model of a formyl group is sufficiently accurate for a Gromos force field, since the alpha proton is very polar and thus may need to be explicitly represented. I have stated my skepticism before but it appears Shima is pursuing the current course. Side note ;) -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@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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-request@. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998870.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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@ http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at
Re: [gmx-users] Re: pdb2gmx error
Dear Justin, All right. I'll give it a try. Thanks Justin. I hope it works and the FOR issue would be terminated Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, June 28, 2012 12:17 AM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 2:42 PM, Shima Arasteh wrote: You are right. OK, the reason of adding FOR is what I explained a few minutes ago. All over, I'm supposed to use a modern FF . ( In similar researches I found CHARMM is suitable, so I would add FOR as the procedure explained in GROMACS.ORG) This sounds like a good idea. For now, because I wanna regenerate an old simulation, I keep the FOR, then here it's stopped! Seeking for a solution! There is one possible solution that I just thought of. Rather than using FOR as its own residue, create a formylated valine, thus eliminating the problem with the call to CA of the preceding residue. The .rtp entry: [ FVAL ] [ atoms ] CN CH1 0.380 0 ON O -0.380 0 N N -0.280 1 H H 0.280 1 CA CH1 0.000 2 CB CH1 0.000 3 CG1 CH3 0.000 4 CG2 CH3 0.000 5 C C 0.380 6 O O -0.380 6 [ bonds ] CN ON CN N N H N CA CA C C O CA CB CB CG1 CB CG2 [ impropers ] N CN CA H CN -CA N ON CA N C CB CB CG2 CG1 CA The .hdb entry: FVAL 1 1 1 H N CN CA Then add FVAL to residuetypes.dat as a protein residue. Processing the .pdb file you posted before (merging FOR and VAL into FVAL and adjusting names according to the .rtp entry above) works correctly. Disclaimer: this method works (i.e. produces a topology) but I do not necessarily endorse the use of the parameters shown. -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
