Re: [gmx-users] Interaction study for peptide-receptor..
Justin, Single mutation for four residue. The number of mutants is 4x19=76 Of course , that is a tiny peptide library. Best Shiyong On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul wrote: > > > On 10/9/12 8:43 PM, Liu Shiyong wrote: >> >> Hi, >> >> Your expectation from MD is too much than reality. >> >> Peptide design is an open problem. Lots of elegant protocols are >> available. However, to my understanding, the core problem is still >> about protein-peptide docking and scoring. MD simulation only helps on >> some special cases. It is impossible that MD simulation is used to for >> screening peptide library. >> > > I would hardly call 4 different mutants a library. Plenty of methods exist > to enhance the sampling of such systems and have been used to great effect. > Computationally expensive to pull off properly? Yes. Impossible? In this > case, I would say no. > > -Justin > > >> >> On Thu, Oct 4, 2012 at 9:16 PM, rama david >> wrote: >>> >>> Thank you for reply, >>> I read the recently published article in Biochemistry. >>> They worked on the same receptor that I am working. >>> ( as I mention in my previous mail) >>> They used NAMD software and I am using gromacs. >>> They sliced the receptor binding site and used the the solid support >>> to the binding site and did simulation. >>> So if I freeze the group is it will ok ?? >>> Is it possible in gromacs to fix the residue on solid immobilized >>> surface. >>> If it is how to do it?? >>> >>> my question is How to decide which group are remove and which group >>> should >>> keep in simulation. >>> >>> thank you in advance >>> Thank you for giving your valuable time and advice to me. >>> >>> With best wishes and regards, >>> Rama david >>> >>> >>> >>> >>> >>> >>> On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis >>> wrote: >>> >>>> I don't think AutoDock and Vina are suitable for peptide docking. I >>>> would >>>> first try the FlexPepDocking module of Rosetta which does ab initio >>>> folding >>>> of the peptide on the receptor, while moving the side-chains of the >>>> protein >>>> but leaves its backbone intact. Rosetta implements a knowledge-based >>>> scoring, which has been specifically designed for this task and is as >>>> fast >>>> as Vina or AutoDock. >>>> >>>> I would first do that and if I wouldn't get any reasonable results then >>>> I >>>> would move to MD starting from the top scored protein-peptide complexes >>>> created by Rosetta. >>>> >>>> Thomas >>>> >>>> >>>> On 4 October 2012 15:08, rama david wrote: >>>> >>>>> Hi francesco, >>>>> >>>>> Thank you For reply. >>>>> I did docking but the result are not so impressive. >>>>> I used vina and autodock. >>>>> I also did virtual screening in autodock but the result are not upto >>>>> the >>>>> mark. >>>>> >>>>> Is the freezing of group can affect my system?? How much efficiency I >>>>> get >>>>> by these work?? >>>>> As these group are going to freeze in four simulation so if it affect >>>>> one >>>>> ligand it affect other >>>>> ligand also. >>>>> >>>>> I read article that did the work like me , >>>>> they sliced the binding residues and used the inert solid sphere to >>>>> support binding residues >>>>> instead of the freezing group other group. >>>>> >>>>> I think both way should have same effect..Am I right or wrong?? >>>>> >>>>> If you have any other way please suggest it.. >>>>> >>>>> With best wishes and regards >>>>> Rama david >>>>> >>>>> >>>>> On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> as far as I know, freezing just set velocities to 0 so you gain >>>>>> nothing >>>>>> freezing atoms. >>>>>> >>>>>> By the way, have you tried docking? It takes into account mu
Re: [gmx-users] Interaction study for peptide-receptor..
Hi, Your expectation from MD is too much than reality. Peptide design is an open problem. Lots of elegant protocols are available. However, to my understanding, the core problem is still about protein-peptide docking and scoring. MD simulation only helps on some special cases. It is impossible that MD simulation is used to for screening peptide library. Best Shiyong On Thu, Oct 4, 2012 at 9:16 PM, rama david wrote: > Thank you for reply, > I read the recently published article in Biochemistry. > They worked on the same receptor that I am working. > ( as I mention in my previous mail) > They used NAMD software and I am using gromacs. > They sliced the receptor binding site and used the the solid support > to the binding site and did simulation. >So if I freeze the group is it will ok ?? > Is it possible in gromacs to fix the residue on solid immobilized surface. > If it is how to do it?? > > my question is How to decide which group are remove and which group should > keep in simulation. > > thank you in advance > Thank you for giving your valuable time and advice to me. > > With best wishes and regards, > Rama david > > > > > > > On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis wrote: > >> I don't think AutoDock and Vina are suitable for peptide docking. I would >> first try the FlexPepDocking module of Rosetta which does ab initio folding >> of the peptide on the receptor, while moving the side-chains of the protein >> but leaves its backbone intact. Rosetta implements a knowledge-based >> scoring, which has been specifically designed for this task and is as fast >> as Vina or AutoDock. >> >> I would first do that and if I wouldn't get any reasonable results then I >> would move to MD starting from the top scored protein-peptide complexes >> created by Rosetta. >> >> Thomas >> >> >> On 4 October 2012 15:08, rama david wrote: >> >> > Hi francesco, >> > >> > Thank you For reply. >> > I did docking but the result are not so impressive. >> > I used vina and autodock. >> > I also did virtual screening in autodock but the result are not upto the >> > mark. >> > >> > Is the freezing of group can affect my system?? How much efficiency I get >> > by these work?? >> > As these group are going to freeze in four simulation so if it affect one >> > ligand it affect other >> > ligand also. >> > >> > I read article that did the work like me , >> > they sliced the binding residues and used the inert solid sphere to >> > support binding residues >> > instead of the freezing group other group. >> > >> > I think both way should have same effect..Am I right or wrong?? >> > >> > If you have any other way please suggest it.. >> > >> > With best wishes and regards >> > Rama david >> > >> > >> > On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri >> > wrote: >> > >> > > Hi, >> > > as far as I know, freezing just set velocities to 0 so you gain nothing >> > > freezing atoms. >> > > >> > > By the way, have you tried docking? It takes into account multiple >> > > conformation and >> > > orientation of the peptide and, depending upon the implemented >> algorithm, >> > > also >> > > protein sidechain orientation. >> > > >> > > Francesco >> > > >> > > >> > > 2012/10/4 rama david >> > > >> > > > thank you Justin for reply. >> > > > >> > > > I dont know about long range interactions. >> > > > But as I freeze the group I think it will improve my computational >> > speed. >> > > > So is there any way to find out or decide which group should be >> > > > freeze, and which group should affect my interaction most probably?? >> > > > >> > > > Should I do Essential Dynamics ??? or Principle component analysis >> ??? >> > > > >> > > > Would you suggest me any general protocol for such work?? >> > > > >> > > > Thank you in Advance >> > > > >> > > > >> > > > With Best Wishes and regards. >> > > > Rama David >> > > > >> > > > On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul >> wrote: >> > > > >> > > > > >> > > > > >> > > > > On 10/4/12 2:01 AM, rama david wrote: >> > > > > >> > > > >> Hi gromacs Friends, >> > > > >> I want to do peptide-receptor ( Protein) interaction >> > > > >> study.Receptor consist a single chain. >> > > > >> Peptide is made up of 4 amino acids. I know the interaction >> > pattern >> > > of >> > > > >> peptide and receptor. >> > > > >> I plan to mutate single residue each at a time and run 4 >> > simulation . >> > > > >> So I will have the 4 different simulation that contain the mutated >> > > > >> residues >> > > > >> and the wild one. >> > > > >> >> > > > >> >> > > > >> Then afterward from the interaction energy I want to select the >> > > peptide >> > > > >> which is showing >> > > > >> stronger interaction than others. >> > > > >> >> > > > >> As mention I know the binding site, If I freeze the remaining >> > portion >> > > > in >> > > > >> receptor >> > > > >> that not involved in binding , Is it going to affect my screening >> > > > process >> > > > >> ??? >> > > > >> >> > > >
Re: [gmx-users] distance between protein and ligand
Hi, Did u repeat your MD simulation of your docked complex ? I also asked the similar question. Alex replied :" I would start several (5-10?) runs with different (random) starting impulse to get more reliable data." Best Shiyong On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani wrote: > Hi, > > I have simulated a protein-ligand complex for 5ns. I checked distance > between the important residues of protein and the ligand using g_dist. My > question is can the distance between the two groups decrease from the > initial distance (docked complex as starting structure for simulation). I > know it may increase or may remain same at the end of the simulation. > > for example: starting distance is 0.77nm and final distance is 0.8nm but > the intermediate course of simulation (around 3ns) it has decreased upto > 0.65. The complex shows stability after 2ns. While the SASA between the two > groups is around 6.3 nm2 throughout the simulation which is very high. > > This is very contradicting result. Is something wrong in the simulation? > > Thanks in advance. > > -- > Archana Sonawani-Jagtap > Junior Research Fellow, > Biomedical Informatics Centre, > NIRRH (ICMR), Parel > Mumbai, India. > 9960791339 > -- > 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 -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] Do I need to repeat my MD simulation ?
Dear all, I did a MD simulation (GROMACS 4.5 G53a6 force field) on protein-peptide complex for 5ns and got an interesting conformational change of T-loop. However, when I rerun my script using the same input file in the same machine, I can not observe the same or similar conformational change. There is a significant difference between two independent run. What could I do for inconsistent MD simulation? Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] PRODRG tools
Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] trjconv problem for two groups
Dear all, I tried to output protein-ligand complex from trr file . Could I select both Group 2 and Group 12 at the same time ? Or I have to run this command for every group , respectively? Select group for output Opening library file /usr/share/gromacs/top//aminoacids.dat Group 0 ( System) has 253787 elements Group 1 ( Protein) has 3403 elements Group 2 ( Protein-H) has 2655 elements Group 3 ( C-alpha) has 328 elements Group 4 (Backbone) has 984 elements Group 5 ( MainChain) has 1313 elements Group 6 (MainChain+Cb) has 1623 elements Group 7 ( MainChain+H) has 1627 elements Group 8 ( SideChain) has 1776 elements Group 9 ( SideChain-H) has 1342 elements Group10 ( Prot-Masses) has 3403 elements Group11 ( Non-Protein) has 250384 elements Group12 ( DRG) has28 elements Group13 ( SOL) has 250356 elements Group14 ( Other) has 250384 elements Select a group: Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] trjconv with superposition
Dear Colleagues,
I want to extract PDB snapshot from trajectory file by following command. It
works in 4.0, but not in 4.5
pdb=1akk
trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc
trjconv -s ${pdb}_gromos53a6_MD2.tpr -f ${pdb}_gromos53a6_MD2.traj.xtc -dt
20 -b 0 -o ${pdb}_gromos53a6_MD2.traj.nojump.pdb -fit rot+trans -pbc nojump
Program trjconv, VERSION 4.5.3
Source code file: gmx_trjconv.c, line: 854
Fatal error:
PBC condition treatment does not work together with rotational fit.
Please do the PBC condition treatment first and then run trjconv in a second
step
for the rotational fit.
First doing the rotational fit and then doing the PBC treatment gives
incorrect
results!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Best
Shiyong
--
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院 生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
---
--
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] Which FF could be used for protein-RNA MD simulation in GROMACS?
I tried amber99 and amber03. I got the same error info : Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.hdb Opening force field file /usr/local/share/gromacs/top/amber03.ff/dna.hdb Opening force field file /usr/local/share/gromacs/top/amber03.ff/rna.hdb Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.n.tdb Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.c.tdb There are 0 donors and 0 acceptors There are 0 hydrogen bonds 8 out of 8 lines of specbond.dat converted successfully Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.arn Opening force field file /usr/local/share/gromacs/top/amber03.ff/dna.arn Opening force field file /usr/local/share/gromacs/top/amber03.ff/rna.arn --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom P in residue G 201 was not found in rtp entry RG5 with 32 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "RTFM" (B. Hess) Using the Amber03 force field in directory amber03.ff Reading 1A1T_amber03.pdb... Read 'SL3 STEM-LOOP RNA; NUCLEOCAPSID PROTEIN', 873 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 3 chains and 0 blocks of water and 57 residues with 873 atoms chain #res #atoms 1 'B'20432 2 'A'55439 3 'A' 2 2 Reading residue database... (amber03) Processing chain 1 'B' (432 atoms, 20 residues) Identified residue G201 as a starting terminus. Identified residue C220 as a ending terminus. -- 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] Which FF could be used for protein-RNA MD simulation in GROMACS?
Sorry. Please skip my info. I found that the problem may be caused by bash . Now, it seems OK. Select the Force Field: >From current directory: 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR >From '/usr/local/share/gromacs/top': 19: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 20: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 21: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 22: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 23: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) 24: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 25: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 26: CHARMM27 all-atom force field (with CMAP) - version 2.0 27: GROMOS96 43a1 force field 28: GROMOS96 43a2 force field (improved alkane dihedrals) 29: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 30: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 31: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 32: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 33: [DEPRECATED] Encad all-atom force field, using full solvent charges 34: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 35: [DEPRECATED] Gromacs force field (see manual) 36: [DEPRECATED] Gromacs force field with hydrogens for NMR On Sat, Dec 11, 2010 at 4:05 PM, Liu Shiyong wrote: > I compiled the new version GROMACS 4.5.3 > and installed according to > http://www.gromacs.org/Downloads/Installation_Instructions > > But I got the following info: > > --- > Program pdb2gmx, VERSION 4.5.3 > Source code file: pdb2top.c, line: 154 > > Fatal error: > No force fields found (files with name 'forcefield.itp' in > subdirectories ending on '.ff') > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > Thanx for Using GROMACS - Have a Nice Day > > > > On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul wrote: >> >> >> Liu Shiyong wrote: >>> >>> Hi, >>> >>> I just tried G53a6 for protein-RNA simulation. But fatal error shows up. >>> >> >> That's a useless description of the problem. Exact input and output would >> be necessary to diagnose the problem. Regardless, the choice of Gromos is a >> particularly bad one for nucleic acid simulations. >> >> http://lists.gromacs.org/pipermail/gmx-users/2010-December/056409.html >> >>> Opening library file /usr/share/gromacs/top//FF.dat >>> >>> Select the Force Field: >> >> You probably don't want any of these force fields. Ask yourself - what do >> you commonly see in the literature? Have similar studies been done? I >> would suggest upgrading to the latest version of Gromacs (4.5.3), which has >> built-in compatibility with CHARMM many AMBER force fields. Then do some >> homework and decide. >> >> -Justin >> >>> 0: GROMOS96 43a1 force field >>> 1: GROMOS96 43a2 force field (improved alkane dihedrals) >>> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) >>> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) >>> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) >>> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) >>> 6: [DEPRECATED] Gromacs force field (see manual) >>> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR >>>
Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?
I compiled the new version GROMACS 4.5.3 and installed according to http://www.gromacs.org/Downloads/Installation_Instructions But I got the following info: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 154 Fatal error: No force fields found (files with name 'forcefield.itp' in subdirectories ending on '.ff') For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanx for Using GROMACS - Have a Nice Day On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: >> >> Hi, >> >> I just tried G53a6 for protein-RNA simulation. But fatal error shows up. >> > > That's a useless description of the problem. Exact input and output would > be necessary to diagnose the problem. Regardless, the choice of Gromos is a > particularly bad one for nucleic acid simulations. > > http://lists.gromacs.org/pipermail/gmx-users/2010-December/056409.html > >> Opening library file /usr/share/gromacs/top//FF.dat >> >> Select the Force Field: > > You probably don't want any of these force fields. Ask yourself - what do > you commonly see in the literature? Have similar studies been done? I > would suggest upgrading to the latest version of Gromacs (4.5.3), which has > built-in compatibility with CHARMM many AMBER force fields. Then do some > homework and decide. > > -Justin > >> 0: GROMOS96 43a1 force field >> 1: GROMOS96 43a2 force field (improved alkane dihedrals) >> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) >> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) >> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) >> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) >> 6: [DEPRECATED] Gromacs force field (see manual) >> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR >> 8: Encad all-atom force field, using scaled-down vacuum charges >> 9: Encad all-atom force field, using full solvent charges >> >> Best >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://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 > -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] Which FF could be used for protein-RNA MD simulation in GROMACS?
Thanks. I will upgrade to Version 4.5 and use AMBER. I like G53a6, but it surprised me without RNA parameter. On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: >> >> Hi, >> >> I just tried G53a6 for protein-RNA simulation. But fatal error shows up. >> > > That's a useless description of the problem. Exact input and output would > be necessary to diagnose the problem. Regardless, the choice of Gromos is a > particularly bad one for nucleic acid simulations. > > http://lists.gromacs.org/pipermail/gmx-users/2010-December/056409.html > >> Opening library file /usr/share/gromacs/top//FF.dat >> >> Select the Force Field: > > You probably don't want any of these force fields. Ask yourself - what do > you commonly see in the literature? Have similar studies been done? I > would suggest upgrading to the latest version of Gromacs (4.5.3), which has > built-in compatibility with CHARMM many AMBER force fields. Then do some > homework and decide. > > -Justin > >> 0: GROMOS96 43a1 force field >> 1: GROMOS96 43a2 force field (improved alkane dihedrals) >> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) >> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) >> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) >> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) >> 6: [DEPRECATED] Gromacs force field (see manual) >> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR >> 8: Encad all-atom force field, using scaled-down vacuum charges >> 9: Encad all-atom force field, using full solvent charges >> >> Best >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://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 > -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] Which FF could be used for protein-RNA MD simulation in GROMACS?
Hi, I just tried G53a6 for protein-RNA simulation. But fatal error shows up. Opening library file /usr/share/gromacs/top//FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Best -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 --- -- 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] Re: gromacs
All 63 kernel tests PASSED Here follows a list of the lines in reference_s.log and ener.log which did not pass the comparison test within tolerance 0.05 Index Reference This test Error Description 11-34.5967-42.0952 0.0977748 1aml.pdb with G53a6 using vsite=none and water=spc 12-34.5967-42.0952 0.0977748 1aml.pdb with G53a6 using vsite=none and water=spce There were 2/45 differences in final energy with the reference file pdb2gmx tests FAILED On Wed, Apr 21, 2010 at 4:36 PM, Liu Shiyong wrote: > Dear all, > > I download gromacs-4.0.5 and installed it. > > I got the test by git. > > git clone git://git.gromacs.org/regressiontests.git > > > then: > > Testing fe_test . . . PASSED > Testing field . . . FAILED. Check checkvir.out (264 errors) files in field > Testing nacl . . . PASSED > Testing sw . . . PASSED > Testing tip4p . . . FAILED. Check checkvir.out (95 errors) files in tip4p > Testing tip4pflex . . . PASSED > Testing urea . . . PASSED > Testing water . . . FAILED. Check checkvir.out (145 errors) files in water > 3 out of 14 complex tests FAILED > > Best > > > -- > Shiyong Liu > -- > Biomolecular Physics and Modeling Group, Department of Physics, > Huazhong University of Science and Technology, Wuhan 430074, Hubei, China > Tel：86-27-87558335-608 > -- > Chinese Version: > -- > 刘士勇 > 华中科技大学物理学院 生物物理模建小组 > 湖北省武汉市洪山区珞瑜路1037号 > 邮编：430074 > 电话：86-27-87558335-606 > --- > -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-608 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-606 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs
Dear all, I download gromacs-4.0.5 and installed it. I got the test by git. git clone git://git.gromacs.org/regressiontests.git then: Testing fe_test . . . PASSED Testing field . . . FAILED. Check checkvir.out (264 errors) files in field Testing nacl . . . PASSED Testing sw . . . PASSED Testing tip4p . . . FAILED. Check checkvir.out (95 errors) files in tip4p Testing tip4pflex . . . PASSED Testing urea . . . PASSED Testing water . . . FAILED. Check checkvir.out (145 errors) files in water 3 out of 14 complex tests FAILED Best -- Shiyong Liu -- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-608 -- Chinese Version: -- 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-606 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy groups
Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title = b cpp = /usr/bin/cpp integrator = cg dt = 0.002; ps ! nsteps = 1 rlist = 0.55 nstlist = 0 vdwtype = Cut-off rvdw= 0.6 coulombtype = Cut-off epsilon_r = 2 rcoulomb= 0.6 energy_grps = chAANDB_&_!H* chC_&_!H* ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 I got the same error. --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 150 Fatal error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups --- "It's Against the Rules" (Pulp Fiction) On Mon, Feb 2, 2009 at 7:05 PM, Mark Abraham wrote: > > Liu Shiyong wrote: >> >> command: >> >> + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro >> + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb >> + editconf -f a6.gro -o a6.gro -d 20.0 >> + make_ndx -f a.pdb -o a6.ndx >> + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr > > > I think you still don't need two invocations of pdb2gmx. Your only constraint > is that you want chain IDs preserved for your make_ndx command. The PDB > format carries the system size just like the GRO format. Thus > > + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb > + editconf -f a6.pdb -o a6.gro -d 20.0 > + make_ndx -f a6.pdb -o a6.ndx > > + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr > > Simpler still is to define your index groups using information other than the > chain ID - as I think someone suggested days ago. Ranges of atom numbers are > also effective. > > >>--- >> Program grompp, VERSION 4.0.2 >> Source code file: grompp.c, line: 150 >> Fatal error: >> atoms 1 and 2 in charge group 1 of molecule type >> 'Protein_A' are >> in different energy groups >> >> --- >> >> >>There is still some sort of disconnect between topology numbering >>(which is where charge groups are defined), and the structure you >>are using. Can you post the first *few* lines of your .pdb file, [ >>atoms ] section of the .top, and the relevant index groups? > > > Not necessarily - the assignment of energy groups in the .mdp file is still a > potential source of problems. > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy groups
18 19 23 24 25 26 27 28 29 30 31 32 34 35 36 37 38 39 40 41 43 44 45 46 48 49 51 52 54 56 58 60 61 62 64 65 66 67 68 69 70 71 72 74 75 76 77 2569 2570 [ chC_&_!H* ] 2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605 2606 2607 On Mon, Feb 2, 2009 at 5:46 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > > Here is my command. >> >> pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o >>a6.gro >> >> pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb >> >> >>Why are you running pdb2gmx twice? Unless you have multiple >>proteins, and need multiple topologies, you should not be doing this. >> >> >> >> That's because the *.gro file does not include chain id information. >> >> If I run make_ndx -f a6.gro -o a6.ndx >> >> I will get : >> >> Found 0 atoms with chain identifiers A AND B >> > >> Found 0 atoms with chain identifier C >> >> > Alright, I was just confused why you're running pdb2gmx twice to get the > desired output. If you need a .pdb file, then just choose it as your output > format the first time you run the command. I would recommend not dealing > with multiple iterations of the same command; it can lead to confusion. > > editconf -f a6.gro -o a6.gro -d 20.0 >> >> >>You realize that the units of -d are nm, right? Do you need such a >>huge solute-box distance? >> >> I know the units is nm. >> > > Just checking :) > > >> > > > >--- >> Program grompp, VERSION 4.0.2 >> Source code file: grompp.c, line: 150 >> Fatal error: >> atoms 1 and 2 in charge group 1 of molecule type >>'Protein_A' are >> in different energy groups >> --- >> > > There is still some sort of disconnect between topology numbering (which is > where charge groups are defined), and the structure you are using. Can you > post the first *few* lines of your .pdb file, [ atoms ] section of the .top, > and the relevant index groups? > > -Justin > > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy groups
On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> >> >> >> pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p >> r-l_365130_G53a6.minim_traj_withH_0.6.top -i >> r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o >> r-l_365130_G53a6.minim_traj_withH_0.6.gro >> >r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 2>&1 >> >> Hi, Justin >> >> >> >> grompp read the coordinate file : a6.gro from the output of editconf. >> editconf read the a6.gro ( output from the first pdb2gmx). >> >> top file a6.top from the output of the first pdb2gmx. >> >> I think the the coordinate file corresponds to the topology file a6.top. >> >> > "Think" is not as definite as "know" - computers are literal, so you must > be, too. > > >> Here is my command. >> >> pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro >> >> pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb >> >> > Why are you running pdb2gmx twice? Unless you have multiple proteins, and > need multiple topologies, you should not be doing this. That's because the *.gro file does not include chain id information. If I run make_ndx -f a6.gro -o a6.ndx I will get : Found 0 atoms with chain identifiers A AND B > Found 0 atoms with chain identifier C > > editconf -f a6.gro -o a6.gro -d 20.0 >> >> > You realize that the units of -d are nm, right? Do you need such a huge > solute-box distance? I know the units is nm. > > make_ndx -f a.pdb -o a6.ndx >> >> > OK, here's the likely problem. If you're running pdb2gmx twice, you are > probably doing different things. So you're making an index file from a .pdb > file that was perhaps treated differently than the .gro file that > corresponds to a6.top. Use the .gro file as input into make_ndx and see if > that alleviates the problem. > > > grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o >> a6.input.tpr >> >> >> > This *should* work, provided the .ndx file is what you actually think it > is, and you are using the correct topology. > > -Justin > > >> >> On Mon, Feb 2, 2009 at 4:28 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >>Alright, so how about the other comment I made? Are you using the >>right coordinate file? I recall you got this error when you used >>the non-pdb2gmx processed .pdb file as input into grompp. You must >>use the coordinate file that corresponds to your topology. >> >>-Justin >> >>Liu Shiyong wrote: >> >>Hi, Justin >>I remove the del command. But I still got an error. >> >>make_ndx -f a.pdb -o a.ndx < make_ndx.input >> >>make_ndx.input: >> >>chain A and B& !a H* >>chain C& !a H* >>q >> >> >> >>checking input for internal consistency... >>Opening library file /export/apps/share/gromacs/top//ffG53a6.itp >>Opening library file /export/apps/share/gromacs/top//ffG53a6nb.itp >>Opening library file /export/apps/share/gromacs/top//ffG53a6bon.itp >>Opening library file /export/apps/share/gromacs/top//ff_dum.itp >>Generated 165 of the 1596 non-bonded parameter combinations >>Opening library file /export/apps/share/gromacs/top//spc.itp >>Opening library file /export/apps/share/gromacs/top//ions.itp >>Excluding 3 bonded neighbours molecule type 'Protein_A' >>Excluding 3 bonded neighbours molecule type 'Protein_B' >>Excluding 3 bonded neighbours molecule type 'Protein_C' >> >>NOTE 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]: >> System has non-zero total charge: -7.02e+00 >> >> >> >>processing coordinates... >>double-checking input for internal consistency... >> >>WARNING 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line >> 39]: >> With nstlist=0 atoms are only put into the box at step 0, >> therefore >> drifting atoms might cause the simulation to crash. >>renumbering atomtypes... >>converting bonded parameters... >>initialising group options... >>processing index file... >>Making dummy/rest group for T-Coupling containing 4655 elements >>Making dummy/rest group for Accele
Re: [gmx-users] energy groups
pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o r-l_365130_G53a6.minim_traj_withH_0.6.gro >r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 2>&1 Hi, Justin grompp read the coordinate file : a6.gro from the output of editconf. editconf read the a6.gro ( output from the first pdb2gmx). top file a6.top from the output of the first pdb2gmx. I think the the coordinate file corresponds to the topology file a6.top. Here is my command. pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb editconf -f a6.gro -o a6.gro -d 20.0 make_ndx -f a.pdb -o a6.ndx grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr On Mon, Feb 2, 2009 at 4:28 PM, Justin A. Lemkul wrote: > > Alright, so how about the other comment I made? Are you using the right > coordinate file? I recall you got this error when you used the non-pdb2gmx > processed .pdb file as input into grompp. You must use the coordinate file > that corresponds to your topology. > > -Justin > > Liu Shiyong wrote: > >> Hi, Justin >> I remove the del command. But I still got an error. >> >> make_ndx -f a.pdb -o a.ndx < make_ndx.input >> >> make_ndx.input: >> >> chain A and B& !a H* >> chain C& !a H* >> q >> >> >> >> checking input for internal consistency... >> Opening library file /export/apps/share/gromacs/top//ffG53a6.itp >> Opening library file /export/apps/share/gromacs/top//ffG53a6nb.itp >> Opening library file /export/apps/share/gromacs/top//ffG53a6bon.itp >> Opening library file /export/apps/share/gromacs/top//ff_dum.itp >> Generated 165 of the 1596 non-bonded parameter combinations >> Opening library file /export/apps/share/gromacs/top//spc.itp >> Opening library file /export/apps/share/gromacs/top//ions.itp >> Excluding 3 bonded neighbours molecule type 'Protein_A' >> Excluding 3 bonded neighbours molecule type 'Protein_B' >> Excluding 3 bonded neighbours molecule type 'Protein_C' >> >> NOTE 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]: >> System has non-zero total charge: -7.02e+00 >> >> >> >> processing coordinates... >> double-checking input for internal consistency... >> >> WARNING 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]: >> With nstlist=0 atoms are only put into the box at step 0, therefore >> drifting atoms might cause the simulation to crash. >> renumbering atomtypes... >> converting bonded parameters... >> initialising group options... >> processing index file... >> Making dummy/rest group for T-Coupling containing 4655 elements >> Making dummy/rest group for Acceleration containing 4655 elements >> Making dummy/rest group for Freeze containing 4655 elements >> Making dummy/rest group for Energy Mon. containing 1045 elements >> Making dummy/rest group for VCM containing 4655 elements >> Number of degrees of freedom in T-Coupling group rest is 13962.00 >> Making dummy/rest group for User1 containing 4655 elements >> Making dummy/rest group for User2 containing 4655 elements >> Making dummy/rest group for XTC containing 4655 elements >> Making dummy/rest group for Or. Res. Fit containing 4655 elements >> Making dummy/rest group for QMMM containing 4655 elements >> T-Coupling has 1 element(s): rest >> Energy Mon. has 3 element(s): chAANDB_&_!H* chC_&_!H* rest >> Acceleration has 1 element(s): rest >> Freeze has 1 element(s): rest >> User1has 1 element(s): rest >> User2has 1 element(s): rest >> VCM has 1 element(s): rest >> XTC has 1 element(s): rest >> Or. Res. Fit has 1 element(s): rest >> QMMM has 1 element(s): rest >> Checking consistency between energy and charge groups... >> >> --- >> Program grompp, VERSION 4.0.2 >> Source code file: grompp.c, line: 150 >> Fatal error: >> atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in >> different energy groups >> --- >> >> >> >> On Fri, Jan 30, 2009 at 5:11 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu Shiyong wrote: >> >>--- >>Program grompp, VERSION 4.0.2 >&
Re: [gmx-users] energy groups
Hi, Justin I remove the del command. But I still got an error. make_ndx -f a.pdb -o a.ndx < make_ndx.input make_ndx.input: chain A and B& !a H* chain C& !a H* q checking input for internal consistency... Opening library file /export/apps/share/gromacs/top//ffG53a6.itp Opening library file /export/apps/share/gromacs/top//ffG53a6nb.itp Opening library file /export/apps/share/gromacs/top//ffG53a6bon.itp Opening library file /export/apps/share/gromacs/top//ff_dum.itp Generated 165 of the 1596 non-bonded parameter combinations Opening library file /export/apps/share/gromacs/top//spc.itp Opening library file /export/apps/share/gromacs/top//ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 3 bonded neighbours molecule type 'Protein_B' Excluding 3 bonded neighbours molecule type 'Protein_C' NOTE 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]: System has non-zero total charge: -7.02e+00 processing coordinates... double-checking input for internal consistency... WARNING 1 [file r-l_365130_G53a6.minim_traj_withH_0.6.top, line 39]: With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash. renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Making dummy/rest group for T-Coupling containing 4655 elements Making dummy/rest group for Acceleration containing 4655 elements Making dummy/rest group for Freeze containing 4655 elements Making dummy/rest group for Energy Mon. containing 1045 elements Making dummy/rest group for VCM containing 4655 elements Number of degrees of freedom in T-Coupling group rest is 13962.00 Making dummy/rest group for User1 containing 4655 elements Making dummy/rest group for User2 containing 4655 elements Making dummy/rest group for XTC containing 4655 elements Making dummy/rest group for Or. Res. Fit containing 4655 elements Making dummy/rest group for QMMM containing 4655 elements T-Coupling has 1 element(s): rest Energy Mon. has 3 element(s): chAANDB_&_!H* chC_&_!H* rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 150 Fatal error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups --- On Fri, Jan 30, 2009 at 5:11 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > > --- >> Program grompp, VERSION 4.0.2 >> Source code file: grompp.c, line: 150 >> >> Fatal error: >> atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in >> different energy groups >> --- >> > > Check your structure to make sure you are using the right coordinate file. > > Try to *not* delete every other group in the index file. Just because you > don't need these groups in your energygrps does not mean they are not > necessary for other functions. > > -Justin > > >> "Can someone please tell Icarus that he's not the only one falling from >> the sky?" (Urban Dance Squad) >> >> :-) G R O M A C S (-: >> >> GROningen Mixture of Alchemy and Childrens' Stories >> >> >> I checked the a.ndx >> >> [ System ] >> 123456789 10 11 12 13 14 15 >> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 >> >> [ chAANDB_&_!H* ] >> 156789 10 11 12 14 15 16 17 18 19 >> 23 24 25 26 27 28 29 30 31 32 34 35 36 37 38 >> >> [ chC_&_!H* ] >> 2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 >> 2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605 2606 2607 >> >> >> >> -- >> Shiyong Liu >> Postdoc >> center for bioinformatics in the university of kansas >> Lab: (785)864-1962 >> Email: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu > shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@ku.edu>) >> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu> >>
[gmx-users] energy groups
Hi, I tried to make energy groups based on chain id and atom type. My purpose is to select atoms in chain A and B without Hydrogen atoms . This is the command: make_ndx -f a.pdb -o a.ndx < make_ndx.input >a.log cat make_ndx.input del 1-9 chain A and B& !a H* chain C& !a H* q And then run grompp and get an error: Making dummy/rest group for User1 containing 4655 elements Making dummy/rest group for User2 containing 4655 elements Making dummy/rest group for XTC containing 4655 elements Making dummy/rest group for Or. Res. Fit containing 4655 elements Making dummy/rest group for QMMM containing 4655 elements T-Coupling has 1 element(s): rest Energy Mon. has 3 element(s): chAANDB_&_!H* chC_&_!H* rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 150 Fatal error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups --- "Can someone please tell Icarus that he's not the only one falling from the sky?" (Urban Dance Squad) :-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories I checked the a.ndx [ System ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 [ chAANDB_&_!H* ] 156789 10 11 12 14 15 16 17 18 19 23 24 25 26 27 28 29 30 31 32 34 35 36 37 38 [ chC_&_!H* ] 2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605 2606 2607 -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile
Thanks.
Summary:
1) *.gro from pdb2gmx has no chain id information
2) pdb2gmx has an option to output pdb file
3) If you want to make groups based on chain id :
pdb2gmx -ignh -ff ${forcefield} -f input.pdb -o a.pdb
make_ndx -f a.pdb -o a.ndx > a.output.make_ndx
4) mdrun has an option to output the minimized structure.
Thanks to all.
On Thu, Jan 29, 2009 at 12:26 PM, Justin A. Lemkul wrote:
>
>
> Liu Shiyong wrote:
>
>
>> *.gro has no chain id information.
>> I can not make energy group(based on chain id) from *.gro file generated
>> by pdb2gmx
>>
>
> See the mail I just sent.
>
>
>
>>
>>
>>3. Don't strip H, just to add them back again :)
>>
>>
>> I have the structure minimized.pdb after EM.
>>
>> minimized.pdb is output from mdrun with -c option.
>>
>> I tried to feed this structure into pdb2gmx.
>> I got an error.
>>
>> Processing chain 1 'A' (5360 atoms, 535 residues)
>> There are 803 donors and 760 acceptors
>> There are 1025 hydrogen bonds
>> Will use HISB for residue 212
>> Will use HISB for residue 223
>> Will use HISB for residue 277
>> Will use HISB for residue 280
>> Will use HISB for residue 374
>> Will use HISB for residue 380
>> Will use HISB for residue 386
>> Will use HISB for residue 398
>> Will use HISB for residue 425
>> Will use HISB for residue 440
>>
>> ---
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421
>>
>> Fatal error:
>> Atom HD1 in residue HISB 212 not found in rtp entry with 14 atoms
>> while sorting atoms. Maybe different protonation state.
>> Remove this hydrogen or choose a different protonation state.
>> Option -ignh will ignore all hydrogens in the input.
>> ---
>>
>>
> Without -ignh, pdb2gmx expects all atoms to present and appropriately
> named. This is one of the more useful error messages, since it tells you
> exactly how to fix the problem.
>
> -Justin
>
> --
>
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
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Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile
On Wed, Jan 28, 2009 at 6:32 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> Hi, >> >> Thank for your helpful reply. >> >> I understand your feeling. If you have time, please see the following. >> >> mdrun has an option to output the final structure(-c). I just knew it >> after reading your post and checked again :< >> Thanks . >> >> Firstly, I run a minimized command to get the minimized structure. >> >> Secondly, based on the minimized structure, I want to do energy >> calculation with some user-defined energy groups. I guest I need to run >> second pdb2gmx. >> >> > I don't think you do. See comments below. > > The command in the Step 1: >> pdb2gmx -ff G53a6 -f r-l_207655_G53a6.pdb -p r-l_207655_G53a6.top -i >> r-l_207655_G53a6.posre.itp -o r-l_207655_G53a6.gro > >> r-l_207655_G53a6.output.pdb2gmx 2>&1 >> em.mdp >> >> title = r-l_207655_G53a6 >> >> cpp = /usr/bin/cpp >> >> define = -DFLEX_SPC >> >> constraints = none >> >> integrator = l-bfgs >> >> dt = 0.002; ps ! >> nsteps = 1 >> >> nstlist = 20 >> >> ns_type = simple >> >> rlist = 1.8 >> >> coulombtype = shift >> >> epsilon_r = 2.0 >> >> rcoulomb= 1.8 >> >> rcoulomb-switch = 1.7 >> >> vdwtype = shift >> >> rvdw= 1.5 >> >> rvdw_switch = 1.4 >> >> > > These are some bizarre cutoffs for use with 53a6, but perhaps you have your > reasons... > > pbc = no >> >> ; >> >> ; Energy minimizing stuff >> >> ; >> >> emtol = 100.0 >> >> emstep = 0.01 >> >> grompp -f em.mdp -c r-l_207655_G53a6.gro -p r-l_207655_G53a6.top -po >> r-l_207655_G53a6.mdout.mdp -o r-l_207655_G53a6.input.tpr > >> r-l_207655_G53a6.output.grompp 2>&1 >> mdrun -nice 0 -v -s r-l_207655_G53a6.input.tpr -o >> r-l_207655_G53a6.minim_traj.trr -c r-l_207655_G53a6.minimized.pdb -e >> r-l_207655_G53a6.minim_ener.edr -g r-l_207655_G53a6.emlog.log> >> r-l_207655_G53a6.output.mdrun 2>&1 >> >> Now, I get an minimized structure: r-l_207655_G53a6.minimized.pdb >> >> Then , I remove the Hydrogen atom in r-l_207655_G53a6.minimized.pdb, >> rename as clean2.pdb >> >> > Why are you removing hydrogens? > > >> *Step 2:* >> Starting structure: clean2.pdb >> >> I am trying to calculate the energy according to energy groups >> >> >> pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i >> clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1 >> >> > This is redundant. In the first pdb2gmx, you processed your structure with > the 53a6 parameter set, adding some polar hydrogens and building a topology. > Then, you stripped the hydrogens. Now you are adding them back. I see no > point in all of these iterations. > > make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input > >> clean2_0.6.output.make_ndx 2>&1 >> >> > Now you're using the original .pdb file (with no hydrogens) to make an > index group. *This is where you are probably going wrong* - you are > carrying out EM steps using a topology that includes H atoms on polar > groups, but you are constructing index groups that correspond to a structure > without H. Therefore, none of the atom numbers will correspond to what you > think they are (or want them to be). > > em.mdp >> >> title = clean2_0.6 >> cpp = /usr/bin/cpp >> integrator = cg >> dt = 0.002; ps ! >> nsteps = 1 >> rlist = 0.55 >> nstlist = 0 >> vdwtype = Cut-off >> rvdw= 0.6 >> coulombtype = shift >> epsilon_r = 2 >> rcoulomb= 0.6 >> > > Again, really bizarre parameters for use with Gromos96. > > rcoulomb-switch = 0.55 >> energy_grps = chB chA >> ; >> ; Energy minimizing stuff >> ; >> emtol = 100.0 >> emstep = 0.01 >> >> >> grompp -maxwarn 10 -f em.mdp -c clea
Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile
Hi, On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham wrote: > Liu Shiyong wrote: > >> Hi, >> > > >> *Step 2:* >> Starting structure: clean2.pdb >> >> I am trying to calculate the energy according to energy groups >> >> >> pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i >> clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1 >> >> make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input > >> clean2_0.6.output.make_ndx 2>& >> > I tried to make energy groups from the "output" (*.gro) from pdb2gmx. > Found 0 atoms with chain identifier B Group is empty > Found 0 atoms with chain identifier A Group is empty That means no chain id information in *.gro, but I have to define the energy groups according to chain id . > >> So here you made some energy groups from the *input* to pdb2gmx. Make it > from the *output* from pdb2gmx and you will be sure things correspond to the > topology *output* from pdb2gmx. It seems rather obvious to me that your > input to make_ndx has all the hydrogens still in it. > > em.mdp >> >> title = clean2_0.6 >> cpp = /usr/bin/cpp >> integrator = cg >> dt = 0.002; ps ! >> nsteps = 1 >> rlist = 0.55 >> nstlist = 0 >> vdwtype = Cut-off >> rvdw= 0.6 >> coulombtype = shift >> epsilon_r = 2 >> rcoulomb= 0.6 >> rcoulomb-switch = 0.55 >> energy_grps = chB chA >> ; >> ; Energy minimizing stuff >> ; >> emtol = 100.0 >> emstep = 0.01 >> >> >> grompp -maxwarn 10 -f em.mdp -c clean2_0.6.gro -n clean2_0.6.ndx -p >> clean2_0.6.top -o clean2_0.6.input.tpr > clean2_0.6.output.grompp 2>&1 >> >> Then, I got an error msg: >> >> >> clean2_0.6.output.grompp >> >> --- >> Program grompp, VERSION 3.3.3 >> Source code file: ../../../../src/kernel/grompp.c, line: 307 >> >> Fatal error: >> atoms 4175 and 4183 in charge group 1767 are in different energy groups >> --- >> >> "God is a DJ" (Faithless) >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu Shiyong wrote: >> >>Hi, >> >>Did you get my script ? >> >>As I said just a few days ago, I don't run jobs for people. I only >>have allocated time on our University's cluster, which I need for >>myself. >> >>That said, it is also very difficult to go through someone's >>scripting, laden with variables that mean nothing to anyone else but >>you, and come up with something meaningful, especially when everyone >>on this list has their own work to be doing. As I've said several >>times, simply posting your command lines with the relevant error >>message(s) is sufficient. >> >>That said, I really have no clue what you're doing with those >>scripts. It appears that you are running pdb2gmx, grompp, and >>mdrun, then using trjconv to dump out the last frame from your >>energy minimization. The last step is certainly not necessary; >>mdrun outputs the lowest-energy coordinates. >> >>Then you are running pdb2gmx again, and creating index groups. I >>don't understand the purpose of the second pdb2gmx call. >> >>The problem you are facing is easily answered with the fact that you >>simply are again using a structure file that does not have the same >> number of atoms as the structure you used to create the index file. >> It appears that your index files simply have two chains of a >>protein, with the highest atom number being 5966. So of course atom >>6415 is missing. The simple fix is to perhaps simplify your naming >>strategy so you can keep it straight, or instead of scripting >>everything and potentially making mistakes, to just run the commands >>interactively until you have everything flowing. >> >>-Justin >> >>I dump a frame from .trr file. >>
Fwd: [gmx-users] Invalid atom number 6415 in indexfile
Hi, Thank for your helpful reply. I understand your feeling. If you have time, please see the following. mdrun has an option to output the final structure(-c). I just knew it after reading your post and checked again :< Thanks . Firstly, I run a minimized command to get the minimized structure. Secondly, based on the minimized structure, I want to do energy calculation with some user-defined energy groups. I guest I need to run second pdb2gmx. The command in the Step 1: pdb2gmx -ff G53a6 -f r-l_207655_G53a6.pdb -p r-l_207655_G53a6.top -i r-l_207655_G53a6.posre.itp -o r-l_207655_G53a6.gro > r-l_207655_G53a6.output.pdb2gmx 2>&1 em.mdp title = r-l_207655_G53a6 cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = l-bfgs dt = 0.002; ps ! nsteps = 1 nstlist = 20 ns_type = simple rlist = 1.8 coulombtype = shift epsilon_r = 2.0 rcoulomb= 1.8 rcoulomb-switch = 1.7 vdwtype = shift rvdw= 1.5 rvdw_switch = 1.4 pbc = no ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 grompp -f em.mdp -c r-l_207655_G53a6.gro -p r-l_207655_G53a6.top -po r-l_207655_G53a6.mdout.mdp -o r-l_207655_G53a6.input.tpr > r-l_207655_G53a6.output.grompp 2>&1 mdrun -nice 0 -v -s r-l_207655_G53a6.input.tpr -o r-l_207655_G53a6.minim_traj.trr -c r-l_207655_G53a6.minimized.pdb -e r-l_207655_G53a6.minim_ener.edr -g r-l_207655_G53a6.emlog.log> r-l_207655_G53a6.output.mdrun 2>&1 Now, I get an minimized structure: r-l_207655_G53a6.minimized.pdb Then , I remove the Hydrogen atom in r-l_207655_G53a6.minimized.pdb, rename as clean2.pdb *Step 2:* Starting structure: clean2.pdb I am trying to calculate the energy according to energy groups pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1 make_ndx -f clean2.pdb -o clean2_0.6.ndx < ./make_ndx.input > clean2_0.6.output.make_ndx 2>&1 em.mdp title = clean2_0.6 cpp = /usr/bin/cpp integrator = cg dt = 0.002; ps ! nsteps = 1 rlist = 0.55 nstlist = 0 vdwtype = Cut-off rvdw= 0.6 coulombtype = shift epsilon_r = 2 rcoulomb= 0.6 rcoulomb-switch = 0.55 energy_grps = chB chA ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 grompp -maxwarn 10 -f em.mdp -c clean2_0.6.gro -n clean2_0.6.ndx -p clean2_0.6.top -o clean2_0.6.input.tpr > clean2_0.6.output.grompp 2>&1 Then, I got an error msg: clean2_0.6.output.grompp --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/grompp.c, line: 307 Fatal error: atoms 4175 and 4183 in charge group 1767 are in different energy groups --- "God is a DJ" (Faithless) On Wed, Jan 28, 2009 at 12:28 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> Hi, >> >> Did you get my script ? >> > > As I said just a few days ago, I don't run jobs for people. I only have > allocated time on our University's cluster, which I need for myself. > > That said, it is also very difficult to go through someone's scripting, > laden with variables that mean nothing to anyone else but you, and come up > with something meaningful, especially when everyone on this list has their > own work to be doing. As I've said several times, simply posting your > command lines with the relevant error message(s) is sufficient. > > That said, I really have no clue what you're doing with those scripts. It > appears that you are running pdb2gmx, grompp, and mdrun, then using trjconv > to dump out the last frame from your energy minimization. The last step is > certainly not necessary; mdrun outputs the lowest-energy coordinates. > > Then you are running pdb2gmx again, and creating index groups. I don't > understand the purpose of the second pdb2gmx call. > > The problem you are facing is easily answered with the fact that you simply > are again using a structure file that does not have the same number of atoms > as the structure you used to create the index file. It appears that your > index files simply have two chains of a protein, with the highest atom > number being 5966. So of course atom 6415 is missing. The simple fix is to > perhaps simplify your naming strategy so you can keep it straight, or >
[gmx-users] charge groups
Hi, In the manual: " Consider a water molecule interacting with another atom. When we would apply the cutoff an on atom-atom basis we might include the atom-Oxygen interaction(with a charge of -0.82) without the compensating charge of the protons and so induce a large dipole moment over the system. Therefore we have to keep groups of atoms with total charge 0 together. These groups are called charge groups. So, When I tried to define energy groups based on chain id (energy_grps = chA chB) , I always get an error. I don't understand why GROMACS give an option to define energy groups based on chain id. Fatal error: atoms 4176 and 4182 in charge group 1767 are in different energy groups PDB: ATOM 4176 OG SER A 541 -13.599 44.346 39.228 1.00 0.00 S 1 ATOM 4177 N ALA A 542 -12.827 48.211 42.079 1.00 0.00 A 1 ATOM 4178 CA ALA A 542 -12.788 48.960 43.342 1.00 0.00 A 1 ATOM 4179 C ALA A 542 -12.052 50.279 43.097 1.00 0.00 A 1 ATOM 4180 O ALA A 542 -12.096 50.830 41.993 1.00 0.00 A 1 ATOM 4181 CB ALA A 542 -12.084 48.160 44.447 1.00 0.00 A 1 ATOM 1 N THR B 1 22.984 77.078 8.100 1.00 20.55 T N -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Invalid atom number 6415 in indexfile
Hi, Did you get my script ? I dump a frame from .trr file. I did not define xtc-grps On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> Hi, >> >> I got an error when do grompp: The input PDB file comes from the output >> of GROMACS by trajconv command. >> >> > > > --- >> Program grompp, VERSION 3.3.3 >> Source code file: ../../../../src/kernel/readir.c, line: 838 >> >> *Fatal error: >> Invalid atom number 6415 in indexfile* >> --- >> >> > Instead of screen dumps, it would be a lot more useful to see your .mdp > file, as well as the command line (not output from) both grompp and trjconv. > Did you dump the frame from an .xtc file? What did you specify in > xtc-grps? > > -Justin > > -- > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Invalid atom number 6415 in indexfile
Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command. *Here is the log from grompp:* Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c r-l_103703_G53a6.minim_traj_withH_0.6.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n r-l_103703_G53a6.minim_traj_withH_0.6.ndx Input, Opt! Index file -deshuf deshuf.ndx Output, Opt. Index file -p r-l_103703_G53a6.minim_traj_withH_0.6.top InputTopology file -pp processed.top Output, Opt. Topology file -o r-l_103703_G53a6.minim_traj_withH_0.6.input.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -np int1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sortbool no Sort molecules according to X coordinate -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -loadstring Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarn int10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 3 bonded neighbours for Protein_D 1 Excluding 3 bonded neighbours for Protein_E 1 NOTE: System has non-zero total charge: -4.03e+00 processing coordinates... double-checking input for internal consistency... WARNING 1 [file "r-l_103703_G53a6.minim_traj_withH_0.6.top", line 41]: With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash. renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Making dummy/rest group for T-Coupling containing 6415 elements Making dummy/rest group for Acceleration containing 6415 elements Making dummy/rest group for Freeze containing 6415 elements --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 838 *Fatal error: Invalid atom number 6415 in indexfile* --- "Bailed Out Of Edge Synchronization After 10,000 Iterations" (X/Motif) :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... processing topology... # G96BONDS: 6557 # G96ANGLES: 9621 # PDIHS: 3328 # IDIHS: 3469 # LJ14: 10148 *Here is the log from make_ndx:* :-)
[gmx-users] Is there any option to output interaction energy based on energy groups?
Hi, Is there any option to output total interaction energy (without *internal energy*) based on energy groups? *g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr* [shiy...@reco temp20090115]$ g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 4.0.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_energy (-: Option Filename Type Description -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr Input Energy file: edr ene -f2 ener.edr Input, Opt. Energy file: edr ene -s topol.tpr Input, Opt. Run input file: tpr tpb tpa -o energy.xvg Output xvgr/xmgr file -viol violaver.xvg Output, Opt. xvgr/xmgr file -pairspairs.xvg Output, Opt. xvgr/xmgr file -oraorienta.xvg Output, Opt. xvgr/xmgr file -ortorientt.xvg Output, Opt. xvgr/xmgr file -odaorideva.xvg Output, Opt. xvgr/xmgr file -odroridevr.xvg Output, Opt. xvgr/xmgr file -odtoridevt.xvg Output, Opt. xvgr/xmgr file -otenoriten.xvg Output, Opt. xvgr/xmgr file -corr enecorr.xvg Output, Opt. xvgr/xmgr file -vis visco.xvg Output, Opt. xvgr/xmgr file -ravg runavgdf.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]fee bool no Do a free energy estimate -fetemp real 300 Reference temperature for free energy calculation -zeroreal 0 Subtract a zero-point energy -[no]sum bool no Sum the energy terms selected rather than display them all -[no]dp bool no Print energies in high precision -[no]mutot bool no Compute the total dipole moment from the components -[no]uni bool yes Skip non-uniformly spaced frames -skipint0 Skip number of frames between data points -[no]averbool no Print also the X1,t and sigma1,t, only if only 1 energy is requested -nmolint1 Number of molecules in your sample: the energies are divided by this number -ndf int3 Number of degrees of freedom per molecule. Necessary for calculating the heat capacity -[no]flucbool no Calculate autocorrelation of energy fluctuations rather than energy itself -[no]orinst bool no Analyse instantaneous orientation data -[no]ovecbool no Also plot the eigenvectors with -oten -acflen int-1 Length of the ACF, default is half the number of frames -[no]normalize bool yes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum noneFit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or exp9 -ncskip int0 Skip N points in the output file of correlation functions -beginfitreal 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is till the end Opened r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr as single precision energy file Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. --- 1 G96Bond 2 G96Angle 3 Proper-
Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?
Thanks.
I used the PDB file with H . It works though it's still a mystery for me
why PDB file without H couldn't work.
On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul wrote:
>
>
> Liu Shiyong wrote:
>
>
>
> The problem lies here:
>
> Including chain 1 in system: 1296 atoms 125 residues
> Including chain 2 in system: 1274 atoms 123 residues
> Including chain 3 in system: 2085 atoms 201 residues
>
> This suggests that chain 2 (Protein B) should contain numbers up to about
> 2500.
>
> ATOM 1996 O ASN B 248 49.634 9.874 85.195 1.00 0.00
>>ATOM 1997 OXT ASN B 248 50.217 10.536 83.158 1.00 0.00
>>TER
>>ATOM 1998 N GLY C 249 70.273 30.186 73.098 1.00 0.00
>>ATOM 1999 CA GLY C 249 68.973 30.327 72.421 1.00 0.00
>>
>>
> This is the original .pdb file, then? The hydrogens will be missing from
> the appropriate groups in the pdb2gmx-processed output structures. You can
> check the numbering (and pertinent charge groups) in the topology for each
> chain, to be sure.
>
>make_ndx -f ${df}.pdb -o ${file}.ndx >
>>${file}.output.make_ndx
>> << _EOF_
>> del 0-9
>> chain A and B
>> chain C
>> q
>> _EOF_
>>
>
> This should work, with the right input :)
>
> -Justin
>
>
> --
>
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
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Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?
Hi
I have checked the manual, but it did not help. Checking the cgnr column did
not help either.
What I do is just splitting the pdb file into two energy groups (chains A+B
and C). I do not change any definitions of charge groups in Gromacs.
As the result, I am getting "1996 and 1998 are in different energy groups".
ATOM 1996 O ASN B 248 49.634 9.874 85.195 1.00 0.00
ATOM 1997 OXT ASN B 248 50.217 10.536 83.158 1.00 0.00
TER
ATOM 1998 N GLY C 249 70.273 30.186 73.098 1.00 0.00
ATOM 1999 CA GLY C 249 68.973 30.327 72.421 1.00 0.00
As you see, atoms 1996 and 1998 should be in different groups. I have no any
idea whether
it's related to Gromacs or to the pdb file, or to something else? Could
anybody advice SOMETHING?
On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul wrote:
>
>
> Liu Shiyong wrote:
>
>>
>> Hi,
>>
>> I searched the mail list.
>> I found a solution to define energy groups by chain.
>>
>> make_ndx -f ${df}.pdb -o ${file}.ndx > ${file}.output.make_ndx << _EOF_
>> del 0-9
>> chain A and B
>> chain C
>> q
>> _EOF_
>>
>> But , I run
>> grompp -maxwarn 10 -f em.mdp -c ${file}.gro -n ${file}.ndx -p ${file}.top
>> -po ${file}.mdout.mdp -o${file}.input.tpr
>>
>> and got error information:
>>
>> ---
>> Program grompp, VERSION 4.0.2
>> Source code file: grompp.c, line: 150
>>
>> Fatal error:
>> atoms 1996 and 1998 in charge group 296 of molecule type 'Protein_B' are
>> in different energy groups
>> ---
>>
>> I checked my *.ndx file:
>>
>> 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995
>> 1996 1997
>> [ chC ]
>> 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
>> 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027
>>
>>
>> 1996 and 1998 are in different energy groups.
>>
>> What is the meaning of " the charge group 296 of molecule type
>> 'Protein_B' "?
>>
>>
> The manual has information about charge groups. To see exactly what you've
> split apart, check your topology (cgnr column).
>
> -Justin
>
>
>>
>> On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>Liu Shiyong wrote:
>>
>>Hi,
>>
>> We have a protein with two chains A and B. We want to calculate
>>the interaction energy only.
>>Would you advise how to define the energy groups for the chains
>>and how to output the interaction
>>energy between chains A and B ?
>>
>>
>>Have a search of the mailing list archives, similar questions have
>>been dealt with there. Also look in the manual for energy groups in
>>several places.
>>
>>Mark
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
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>>posting!
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>><mailto:gmx-users-requ...@gromacs.org>.
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>>
>>
>>
>>
>> --
>> Shiyong Liu
>> Postdoc
>> center for bioinformatics in the university of kansas
>> Lab: (785)864-1962
>> Email: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu > shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@ku.edu>)
>> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu>
>> Lab:http://vakser.bioinformatics.ku.edu/people
>> Phone: (785) 864-1962
>>
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?
Hi,
I searched the mail list.
I found a solution to define energy groups by chain.
make_ndx -f ${df}.pdb -o ${file}.ndx > ${file}.output.make_ndx << _EOF_
del 0-9
chain A and B
chain C
q
_EOF_
But , I run
grompp -maxwarn 10 -f em.mdp -c ${file}.gro -n ${file}.ndx -p ${file}.top
-po ${file}.mdout.mdp -o${file}.input.tpr
and got error information:
---
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1996 and 1998 in charge group 296 of molecule type 'Protein_B' are in
different energy groups
---
I checked my *.ndx file:
1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995
1996 1997
[ chC ]
1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027
1996 and 1998 are in different energy groups.
What is the meaning of " the charge group 296 of molecule type
'Protein_B' "?
On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham wrote:
> Liu Shiyong wrote:
>
>> Hi,
>>
>> We have a protein with two chains A and B. We want to calculate the
>> interaction energy only.
>> Would you advise how to define the energy groups for the chains and how to
>> output the interaction
>> energy between chains A and B ?
>>
>
> Have a search of the mailing list archives, similar questions have been
> dealt with there. Also look in the manual for energy groups in several
> places.
>
> Mark
> ___
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> Please search the archive at http://www.gromacs.org/search before posting!
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>
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
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[gmx-users] Qestion about how to define groups by chain id in a protein ?
Hi, We have a protein with two chains A and B. We want to calculate the interaction energy only. Would you advise how to define the energy groups for the chains and how to output the interaction energy between chains A and B ? -- Shiyong Liu Postdoc center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv chaged the chain names of multi-chain complex?
Hi,
Chain name is very important for some application. But, when I use the
following script to get a minimized structure from a multi-chain complex.
But the chain name was changed. I checked the man trjconv , but I did not
find any information on chain name for trjconv.
pdb2gmx -ff ${forcefield} -f starting.pdb -p ${file}.top -i
${file}.posre.itp -o ${file}.gro > ${file}.output.pdb2gmx 2>&1
mdrun -nice 0 -v -s ${file}.input.tpr -o ${file}.minim_traj.trr -c
${file}.minimized.gro -e ${file}.minim_ener.edr -g ${file}.emlog.log>
${file}.output.mdrun 2>&1
trjconv -sep -f ${file}.minim_traj.trr -s ${file}.input.tpr -o output.pdb
<< HHH
2
2
HHH
The starting.pdb has four chain: A B D E
The output file output.pdb has a different chain name: A B C D.
Thanks
--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
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[gmx-users] amber force field problem: ignh doesnot work
Hi, I install amber force filed according to source: http://chemistry.csulb.edu/ffamber/index.html But , I run pdb2gmx, I got a problem. Program pdb2gmx, VERSION 3.3.1 pdb2gmx -ignh -ff amber99 -f r-l_1.pdb Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99.rtp Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//aminoacids.dat Reading r-l_1.pdb... Read 3609 atoms Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 3 chains and 0 blocks of water and 449 residues with 3609 atoms chain #res #atoms 1 'A' 125 1006 2 'B' 123991 3 'C' 201 1612 WARNING: there were 22 atoms with zero occupancy and 0 atoms with occupancy unequal to one (out of 3609 atoms). Check your pdb file. Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99.atp Atomtype 73 Reading residue database... (ffamber99) Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99.rtp Residue 132 Sorting it all out... Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99.hdb Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99-n.tdb Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//ffamber99-c.tdb Processing chain 1 'A' (1006 atoms, 125 residues) There are 184 donors and 188 acceptors There are 306 hydrogen bonds Will use HISB for residue 15 Will use HISA for residue 64 Will use HISB for residue 71 Will use HISB for residue 98 Will use HISB for residue 122 Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Checking for duplicate atoms Now there are 1005 atoms. Deleted 1 duplicates. Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Special Atom Distance matrix: CYS36 CYS78 SG297 SG627 CYS78 SG627 1.318 CYS112 SG896 0.969 1.027 N-terminus: none C-terminus: none Now there are 125 residues with 1842 atoms Chain time... Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISA' not found in residue topology database, trying to use 'HID' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Warning: 'LYSH' not found in residue topology database, trying to use 'LYN' Warning: 'HISB' not found in residue topology database, trying to use 'HID' Making bonds... Opening library file /export/apps/gromacs-3.3.1-Amber /share/gromacs/top//aminoacids.dat WARNING: atom H is missing in residue ASP 1 in the pdb file You might need to add atom H to the hydrogen database of residue ASP in the file ff???.hdb (see the manual) WARNING: atom H is missing in residue LYSH 2 in the pdb file You might need to add atom H to the hydrogen database of residue LYSH in the file ff???.hdb (see the manual) WAR
[gmx-users] converged to Epot
Hi, Now, I do minimization. It's converged to Fmax < 100. How can I change it into Epot ? For example, Epot(n)-Epot(n-1) / Epot(n-1) < 5% n is the step. Step= 1891, Dmax= 1.2e-03 nm, Epot= -4.08327e+04 Fmax= 1.31834e+03, atom= 6946 Step= 1892, Dmax= 1.5e-03 nm, Epot= -4.08334e+04 Fmax= 9.46617e+02, atom= 6946 Best -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to change the default value for pbc ?
Thanks.
It's exactly what you said.
ePBC = no
On Thu, Mar 13, 2008 at 6:44 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
> Editing mdout.mdp will not affect the parameters in your .tpr, and
> therefore your simulation, I'm fairly sure. It's just a report of what
> you've specified, with all the defaults.
> Add the pbc=whatever line into your INPUT mdp to fix this.
>
> ----- Original Message
> From: Liu Shiyong <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users
> Sent: Thursday, March 13, 2008 11:39:46 PM
> Subject: [gmx-users] How to change the default value for pbc ?
>
> Hi,
>
> I generated mdout.mdp
>
> by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o
> ${file}.input.tpr .
>
> The pbc in mdout.mdp is like:
>
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
>
> It seems that grompp doesnot give an option to change the pbc value.
>
> I didnot find an easy way to change the pbc value . The only way I found
> is to edit the mdout.mdp directly.
>
> Best
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
> Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu>
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> -Inline Attachment Follows-
>
> ___
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>
>
> --
> Never miss a thing. Make Yahoo your
> homepage.<http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs>
>
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--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
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[gmx-users] How to change the default value for pbc ?
Hi,
I generated mdout.mdp
by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o ${file}.input.tpr
.
The pbc in mdout.mdp is like:
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
It seems that grompp doesnot give an option to change the pbc value.
I didnot find an easy way to change the pbc value . The only way I found is
to edit the mdout.mdp directly.
Best
--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
___
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] trjconv output at a specified time
Thanks. The trajectory starts at 125ps ? So step 1 == 125 ps step 2 == 250 ps step 3 == 375 ps Where is 125ps from ? But ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.002 On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > You asked for the frame at 1ps. The trajectory starts at 125ps, so > unsurprisingly the program does not give you an output. > > - Original Message > From: Liu Shiyong <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Wednesday, March 12, 2008 10:07:17 PM > Subject: [gmx-users] trjconv output at a specified time > > Hi, > > I want to output a structure in a given time, for example , in step 1 > during minimization. > > I tried the following command using dump: > trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s > r-l_1_oplsaa.input.tpr -t0 0 -dump 1 > > But It didnot work. > > Output msg: > > Select a group: 2 > Selected 2: 'Protein-H' > trn version: GMX_trn_file (single precision) > Reading frame 0 time 125.000 > Back Off! I just backed up m.pdb to ./#m.pdb.1# > Last frame 19 time 2418.000 > > WARNING no output, trajectory ended at 2418 > > > gcq#76: "Baseball Heroes Only" (P.J. Harvey) > > Best > > -- > Shiyong Liu > Research Assistant > center for bioinformatics in the university of kansas > Lab: (785)864-1962 > Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) > Homepage: http://www.people.ku.edu/~syliu<http://www.people.ku.edu/%7Esyliu> > Lab: http://vakser.bioinformatics.ku.edu/people > Phone: (785) 864-1962 > > > -Inline Attachment Follows- > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > __ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv output at a specified time
Hi, I want to output a structure in a given time, for example , in step 1 during minimization. I tried the following command using dump: trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s r-l_1_oplsaa.input.tpr -t0 0 -dump 1 But It didnot work. Output msg: Select a group: 2 Selected 2: 'Protein-H' trn version: GMX_trn_file (single precision) Reading frame 0 time 125.000 Back Off! I just backed up m.pdb to ./#m.pdb.1# Last frame 19 time 2418.000 WARNING no output, trajectory ended at 2418 gcq#76: "Baseball Heroes Only" (P.J. Harvey) Best -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] parameter on Energy Minimization
Thanks Mark and Justin.
I did experiment with the following editconf.It works. Thanks.
editconf -f ${file}.gro -o ${file}_box.gro -d 0.75 -bt cubic
By the way, how to select box size automatically ? I just gave an
arbitrary number: 0.75
Another question is how to get the structure with lowest energy from
*.trr ?
When I used the following command:
trjconv -f ${file}.minim_traj.trr -s ${file}.input.tpr -o
${file}.minim_traj.pdb
It outputs 15 MODELS with t= 125.0 t= 252.0, t= 379.0 ,
...t= 2001.0
I guess t= 2001.0 has the lowest energy.
Best
On Tue, Mar 11, 2008 at 5:58 PM, Mark Abraham <[EMAIL PROTECTED]>
wrote:
> > Hi,
> >
> > I used a script given below for energy minimization of a native
> > protein-protein complex 1akj.
> >
> > I removed HETATMs and water molecules from the structure, and the
> > minimized
> > structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80.
> > Then I used rasmol to check the result. The ligand is ran away from
> > receptor.
> > rasmol 1akj_oplsaa.minim_traj.pdb
>
> As Justin said, you might well be observing a PBC artefact. Having not
> turned off PBC in your .mdp file, or used editconf to change the size of
> the box that pdb2gmx chooses, then your EM is probably using defaults that
> you'd rather not use.
>
> > Then I tried the larger epsilon_r = 80.0, and got very
> > similar result. I mean that for two substantially different values of
> the
> > epsilon_r minimization gives absolutely the same final positions of the
> > ligand.
>
> Being good scientists, we deduce that the approximate location of the
> local energy minimum from this starting point is not dependent on the
> dielectic of the medium. :-)
>
> > I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1,
> > G45a3, G53a5, G53a6, gmx, oplsaa.
> > I also got similar result.
>
> Likewise.
>
> Mark
>
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--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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[gmx-users] parameter on Energy Minimization
Hi, I used a script given below for energy minimization of a native protein-protein complex 1akj. I removed HETATMs and water molecules from the structure, and the minimized structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80. Then I used rasmol to check the result. The ligand is ran away from receptor. rasmol 1akj_oplsaa.minim_traj.pdb Then I tried the larger epsilon_r = 80.0, and got very similar result. I mean that for two substantially different values of the epsilon_r minimization gives absolutely the same final positions of the ligand. I also tried difference forcefield encads, encadv, G43a1, G43a2, G43b1, G45a3, G53a5, G53a6, gmx, oplsaa. I also got similar result. script: pdb2gmx -ff oplsaa -f 1akj_oplsaa.pdb -p 1akj_oplsaa.top -o 1akj_oplsaa.gro -i 1akj_oplsaa.itp > 1akj_oplsaa. output.pdb2gmx 2>&1 & grompp -f em.mdp -c 1akj_oplsaa.gro -p 1akj_oplsaa.top -o 1akj_oplsaa.input.tpr > 1akj_oplsaa.output.grompp 2>&1 & mdrun -nice 0 -v -s 1akj_oplsaa.input.tpr -o 1akj_oplsaa.minim_traj.trr -c 1akj_oplsaa.minimized.gro -e 1akj_oplsaa. minim_ener.edr > 1akj_oplsaa.output.mdrun 2>&1 & trjconv -f 1akj_oplsaa.minim_traj.trr -s 1akj_oplsaa.input.tpr -o 1akj_oplsaa.minim_traj.pdb << HHH 2 2 HHH em.mdp is : title = 1akj_oplsaa cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 100 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off epsilon_r = 80.0 rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.8 ; ; Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] minimized on protein-protein decoys
Hi, Mark, Thanks for reply. On Sun, Mar 9, 2008 at 1:41 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Liu Shiyong wrote: > > Hi, all > > > > My purpose is to get the binding energy by gromacs. > > You can't do this without water. The binding energy involves displacing > water interactions. > Yes, But I just tried to get the binding energy by minimizing protein-protein decoy without water. > > > I tried to minimize protein-protein docking decoy by using gromacs > > without water. But after being minimized, the ligand ran away from > > receptor. > > "ran away" during what calculation? > During minimizing ... The following is my script. r-l_1.pdb is a protein-protein decoy structure. pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing > output.pdb2gmx 2>&1 & grompp -f em.mdp -c r-l_1.gro -p r-l_1.top -o input.tpr > output.grompp 2>&1 & mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr > output.mdrun 2>&1 & > > That's not what I expected . I just want to relax the protein-protein > > interface due to some atom-atom contact crash . > > That's what position-restrained EM or MD is for. > Yes, I will try position-restrained EM. Thanks for suggestion. > > By the way, I found the net charge is not zero after adding H atoms on > > complex by pdb2gmx. Can I solve the non-zero net charge problem by > > adding H atom on receptor and ligand > > > > separately? > > Depends what's causing the non-zero charge. Integral non-zero charge is > different from non-integral. Some integral charges are sensible, some > aren't. > The method of adding H atom that I used is pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing > output.pdb2gmx 2>&1 & It added all H atom on receptor and ligand at the same time. Is it a possible reason for Integral non-zero charge ? I want to try to add H atom on receptor and ligand , separately. Do you know how to add H atom on receptor and ligand , separately , and combine them into one input file as minimizing ? If I was wrong, please point out my mistake. Thanks. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) Homepage: http://www.people.ku.edu/~syliu Lab:http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] minimized on protein-protein decoys
Hi, all My purpose is to get the binding energy by gromacs. I tried to minimize protein-protein docking decoy by using gromacs without water. But after being minimized, the ligand ran away from receptor. That's not what I expected . I just want to relax the protein-protein interface due to some atom-atom contact crash . By the way, I found the net charge is not zero after adding H atoms on complex by pdb2gmx. Can I solve the non-zero net charge problem by adding H atom on receptor and ligand separately? Any tip is appreciated. Best shiyong ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
