[gmx-users] Usually how do you decide the salt concentration?
Dear all, Usually how do you decide the salt concentration of the system? I got a protein structure from PDB, and what I am doing now is: to find out from which species the protein is extracted, and then search in google for the normal salt concentration of that species. However, it's hard to find the normal salt concentration. I will appreciate if you can share with me how you decide what the salt concentration. Thanks! Peggy ___ 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] Problem with adding H using amber03
Dear all, I am trying to use amber03 force field. I corrected the amino acid names as described on http://chemistry.csulb.edu/ffamber/. However, when I ran pdb2gmx on a PDB file without H-atoms, I got the following error: pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb ... WARNING: atom H is missing in residue THR 1 in the pdb file You might need to add atom H to the hydrogen database of residue THR in the file ff???.hdb (see the manual) --- Program pdb2gmx, VERSION 4.0.2 Source code file: pdb2top.c, line: 701 Fatal error: There were 1 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing --- I checked the ffamber03.hdb. It is in the correct directory as other *.hdb files. It also contains the entry for H-atom in THR: THR 5 1 1 H N -C CA 1 5 HA CA N CB C 1 5 HB CB CA CG2 OG1 3 4 HG2 CG2 CB CA 1 2 HG1 OG1 CB CA Can anyone tell me what might be the problem? I should be able to use pdb2gmx and amber03 to add all H-atoms, right? Thanks! Peggy ___ 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] Number of processors in parallel running
Thank you, Justin. I am using GMX 4.0.2. Do I need to have the -np option in all grompp and mdrun commands? Thanks in advance! Peggy On Tue, Feb 17, 2009 at 3:02 PM, Justin A. Lemkul wrote: > > > Peggy Yao wrote: > >> Dear all, >> >> In order to run Gromacs on multiple processors, I should put the number of >> processors in the commands. For example, >> >> grompp -np -o topol.tpr >> >> > Only if you're using GMX < 4.0. > > >> My question is: nr should be the number of processors, or the number of >> cores? If I have a quad-core processor, should I put 4? >> >> > Number of cores. Try it and you will see. > > -Justin > > Thanks, >> Peggy >> >> >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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 > ___ 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] Which force field to use to study intra-molecular hydrogen bonding?
Dear all, I'd like to study intra-molecular hydrogen bonding. Which force field would you recommend? I have been working on G43a1 and OPLS. OPLS seems quite good. It places all H-atoms. However, G43a1 only considers H-atoms on N-atoms, but not C-atoms. Even if I input a fully-added-H-atom PDB file to pdb2gmx: pdb2gmx -ff G43a1 -f 1eia_hadded.pdb -p 1eia.top -o 1eia.pdb -water spce 1eia.pdb still only constains H-atoms on N-atoms. I believe, by default, "-ignh" has value "no", which means if I don't put "-ignh", it should read in all the H-atoms in the input PDB file. Besides OPLS, is there any other good force field to study hydrogen bonding? Is there any way to make G43a1 to take all H-atoms into account? Thanks a lot! Peggy ___ 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] Number of processors in parallel running
Dear all, In order to run Gromacs on multiple processors, I should put the number of processors in the commands. For example, grompp -np -o topol.tpr My question is: nr should be the number of processors, or the number of cores? If I have a quad-core processor, should I put 4? Thanks, Peggy ___ 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] Difference between command pdb2gmx and pdb2gmx_d
Dear all, In the manual, almost all commands have 2 versions: command and command_d. For example, pdb2gmx, and pdb2gmx_d. What is the difference? I searched in both the manual and the internet, but was not able to find the answer. Thanks! Peggy ___ 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] Atom index overflow after adding water
Thank you, Justin! I found the error message which was embedded in a lot of text. :P As you said, the atom indexing is not a problem at all. The actual error is: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented When I changed ns_type to grid, the problem was solved! Thanks a lot! Peggy On Sat, Feb 14, 2009 at 4:26 PM, Justin A. Lemkul wrote: > > > Peggy Yao wrote: > >> Unfortunately, no. :( When I tried to add ions to the system using: >> >> grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >> >> It return me an error without explanation: >> >> processing coordinates... >> double-checking input for internal consistency... >> >> There was 1 note >> >> --- >> Program grompp, VERSION 4.0.2 >> Source code file: grompp.c, line: 864 >> >> Fatal error: >> There were 1 error(s) processing your input >> --- >> >> Did I make any mistake? I am new to MD simulation and Gromacs. The >> following are all the steps that I ran until the fatal error: >> >> > Probably. Search the entire output of grompp for the error message. I > don't remember grompp ever reporting a fatal error without printing the > actual problem somewhere that the user can see. > > If you can provide that information, as well as the contents of your .mdp, > there may be a chance to diagnose what's going on. As I said before, the > problem *shouldn't* be the number of atoms in the file. > > -Justin > > pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water >> spce >& pdb2gmx.log >> # add water >> editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log >> genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& >> genbox.log >> # add counter ions >> grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >& >> grompp_ion.log >> >> Peggy >> >> On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham >> > mark.abra...@anu.edu.au>> wrote: >> >> >> >>- Original Message - >>From: Peggy Yao mailto:peggy@gmail.com>> >>Date: Sunday, February 15, 2009 10:24 am >>Subject: Re: [gmx-users] Atom index overflow after adding water >>To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for >>GROMACS users mailto:gmx-users@gromacs.org>> >> >> > Thank you, Justin! >> > >> > I changed the output files to .gro. >> > >> > pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o >>1eia.gro -water spce >& pdb2gmx.log >> > # add water >> > editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log >> > >>genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& >>genbox.log >> > >> > However, the overflow error still occurs in the gro file: >> > >> > 32448SOLHW26 9.410 8.282 1.575 >> > 32449SOL OW7 9.923 8.813 0.726 >> > >>32449SOLHW18 9.874 8.726 0.735 >> > 32449SOLHW29 9.900 8.856 0.639 >> > 32450SOL OW0 0.018 7.452 0.502 >> > 32450SOLHW11 0.058 7.543 0.493 >> > 32450SOLHW22 -0.082 7.460 0.508 >> > >>32451SOL OW3 9.507 8.424 1.264 >> > 32451SOLHW14 9.596 8.379 1.250 >> > >> > What's wrong? Thanks a lot! >> >>Probably nothing. The issue is whether the parsing algorithm in >>grompp will handle the situation gracefully. Justin thinks it does. >>You should try it and see :-) >> >>Mark >>___ >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before >>posting! >>Please don't post (un)subscribe requests to the list. Use the >>www interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >>
Re: [gmx-users] Atom index overflow after adding water
Unfortunately, no. :( When I tried to add ions to the system using: grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr It return me an error without explanation: processing coordinates... double-checking input for internal consistency... There was 1 note --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 864 Fatal error: There were 1 error(s) processing your input --- Did I make any mistake? I am new to MD simulation and Gromacs. The following are all the steps that I ran until the fatal error: pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water spce >& pdb2gmx.log # add water editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& genbox.log # add counter ions grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >& grompp_ion.log Peggy On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham wrote: > > > - Original Message - > From: Peggy Yao > Date: Sunday, February 15, 2009 10:24 am > Subject: Re: [gmx-users] Atom index overflow after adding water > To: jalem...@vt.edu, Discussion list for GROMACS users < > gmx-users@gromacs.org> > > > Thank you, Justin! > > > > I changed the output files to .gro. > > > > pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water > spce >& pdb2gmx.log > > # add water > > editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log > > > genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& > genbox.log > > > > However, the overflow error still occurs in the gro file: > > > > 32448SOLHW26 9.410 8.282 1.575 > > 32449SOL OW7 9.923 8.813 0.726 > > > 32449SOLHW18 9.874 8.726 0.735 > > 32449SOLHW29 9.900 8.856 0.639 > > 32450SOL OW0 0.018 7.452 0.502 > > 32450SOLHW11 0.058 7.543 0.493 > > 32450SOLHW22 -0.082 7.460 0.508 > > > 32451SOL OW3 9.507 8.424 1.264 > > 32451SOLHW14 9.596 8.379 1.250 > > > > What's wrong? Thanks a lot! > > Probably nothing. The issue is whether the parsing algorithm in grompp will > handle the situation gracefully. Justin thinks it does. You should try it > and see :-) > > 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 > ___ 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] Atom index overflow after adding water
Thank you, Justin! I changed the output files to .gro. pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water spce >& pdb2gmx.log # add water editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& genbox.log However, the overflow error still occurs in the gro file: 32448SOLHW26 9.410 8.282 1.575 32449SOL OW7 9.923 8.813 0.726 32449SOLHW18 9.874 8.726 0.735 32449SOLHW29 9.900 8.856 0.639 32450SOL OW0 0.018 7.452 0.502 32450SOLHW11 0.058 7.543 0.493 32450SOLHW22 -0.082 7.460 0.508 32451SOL OW3 9.507 8.424 1.264 32451SOLHW14 9.596 8.379 1.250 What's wrong? Thanks a lot! Peggy On Sat, Feb 14, 2009 at 2:40 PM, Justin A. Lemkul wrote: > > > Peggy Yao wrote: > >> Dear all, >> >> Has anyone encountered the problem of atom index overflow in PDB files >> after adding water molecules? >> >> The following are what I did: >> >> pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.pdb -water >> spce >& pdb2gmx.log >> # add water >> editconf -bt cubic -f 1eia.pdb -o 1eia.pdb -c -d 0.9 >& editconf.log >> genbox -cp 1eia.pdb -cs spc216.gro -o 1eia_water.pdb -p 1eia.top >& >> genbox.log >> >> However, in 1eia_water.pdb, the atom index of the water section >> overflowed: >> >> ATOM 6 HW2 SOL 2448 98.583 52.132 64.542 1.00 0.00 >> ATOM 7 OW SOL 2449 1.182 45.201 68.242 1.00 0.00 >> ATOM 8 HW1 SOL 2449 1.592 44.881 69.102 1.00 0.00 >> ATOM 9 HW2 SOL 2449 0.222 44.931 68.212 1.00 0.00 >> ATOM 0 OW SOL 2450 93.503 42.681 67.002 1.00 0.00 >> ATOM 1 HW1 SOL 2450 94.353 42.351 66.592 1.00 0.00 >> ATOM 2 HW2 SOL 2450 93.633 42.831 67.982 1.00 0.00 >> ATOM 3 OW SOL 2451 94.993 42.441 73.082 1.00 0.00 >> >> How to solve this problem? >> >> > Well, the .pdb file format can only handle a fixed amount of digits when > numbering atoms. I don't know if using .gro format will be of any use, but > I routinely simulate systems of 200,000+ atoms with no problem, and any > index files I make are correctly numbered. > > -Justin > > Thanks, >> Peggy >> >> >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > 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 > ___ 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] Atom index overflow after adding water
Dear all, Has anyone encountered the problem of atom index overflow in PDB files after adding water molecules? The following are what I did: pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.pdb -water spce >& pdb2gmx.log # add water editconf -bt cubic -f 1eia.pdb -o 1eia.pdb -c -d 0.9 >& editconf.log genbox -cp 1eia.pdb -cs spc216.gro -o 1eia_water.pdb -p 1eia.top >& genbox.log However, in 1eia_water.pdb, the atom index of the water section overflowed: ATOM 6 HW2 SOL 2448 98.583 52.132 64.542 1.00 0.00 ATOM 7 OW SOL 2449 1.182 45.201 68.242 1.00 0.00 ATOM 8 HW1 SOL 2449 1.592 44.881 69.102 1.00 0.00 ATOM 9 HW2 SOL 2449 0.222 44.931 68.212 1.00 0.00 ATOM 0 OW SOL 2450 93.503 42.681 67.002 1.00 0.00 ATOM 1 HW1 SOL 2450 94.353 42.351 66.592 1.00 0.00 ATOM 2 HW2 SOL 2450 93.633 42.831 67.982 1.00 0.00 ATOM 3 OW SOL 2451 94.993 42.441 73.082 1.00 0.00 How to solve this problem? Thanks, Peggy ___ 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] Missing atom error when using some force fields
Dear all, I am new to MD simulation. I am trying to do an all-atom MD simulation with explicit water of a protein which has a few missing side-chain atoms of a GLN residue. 1. Which force field would you recommend? The protein is an x-ray crystal structure, about 200 residues. Hydrogen atoms and hydrogen bonding are important. 2. According to the Gromacs manual, OPLS is recommended for all-atom MD simulation. However, when I tried to use OPLS-AA as the force field, pdb2gmx returned me an error: Fatal error: Atom CG not found in residue GLN82 while adding hydrogens Then I tried all other force fields. Only the following didn't give that error: 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) 6: [DEPRECATED] Gromacs force field (see manual) Is any of them good enough? If not, is there any way (such as a good free software) to fill in the missing atoms? Thanks a lot! Peggy ___ 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] Why my system collapsed?
Dear all, I've run this simulation twice, but got exactly the same error. Everything was fine up to position restrained simulation. However, the MD simulation was not successful. The final error is: --- Program mdrun, VERSION 3.3.2 Source code file: nsgrid.c, line: 220 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. --- Starting from step 1749465 (3498.93 ps), more and more bonds that rotated more than 30 degrees appeared. Starting from step 1749466, the warning "pressure scaling more than 1%, mu: 1.27191e+06 1.27191e+06 1.27191e+06" started to appear, and the system collapsed at step 1749467. Does anyone have idea what might be wrong? I was simulating a calcium-binding protein with calcium atoms in water for 4ns. Thanks! Peggy ___ 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] Bad .tpr or .xtc files?
Thank you, Tsjerk. I will check them out. But I am still confursed with what has gone wrong. As I said in my previous eamil, in fact, 2 Ca atoms are a part of the protein. They are in the PDB file passed to pdb2gmx. Water molecules are added after the protein atoms and the Ca atoms, as in the PDB file after genbox. So I suppose, in the .tpr file, atoms should be ordered as protein-Ca-water-Cl? If so, I don't know why when writing out Ca or Cl atoms, I got segmentation fault and index out of bound errors. Peggy On Fri, Apr 11, 2008 at 12:25 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Peggy, > > This is very much basic stuff for which you should refer to the > manual/wiki. E.g. on the index file, look at > > http://wiki.gromacs.org/index.php/Index_File > > For the other questions, check the manpages of editconf, trjconv and > tpbconv. > > Cheers, > > Tsjerk > > On Thu, Apr 10, 2008 at 11:03 PM, Peggy Yao <[EMAIL PROTECTED]> wrote: > > Thank you for the explanation! > > > > In fact, 2 Ca atoms are a part of the protein. They are in the PDB file > > passed to pdb2gmx. Water molecules are added after the protein atoms and > the > > Ca atoms, as in the PDB file after genbox. So I suppose, in the .tpr > file, > > atoms should be ordered as protein-Ca-water-Cl? > > > > If I still have to do what you suggested, could you kindly tell me: > > 1. what is an index file? > > 2. how to make an index file to extract the matching set of atoms from > .tpr > > file? > > 3. how to write a matching reference structure? > > > > Thanks a lot! > > > > Peggy > > > > > > > > On Thu, Apr 10, 2008 at 11:52 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> > > wrote: > > > Hi Peggy, > > > > > > The key thing is that there's a mismatch between your .tpr file and > > > your .xtc file. The first is used for the indexing and it may very > > > well be that there's stuff in between the protein and the calcium. > > > That way, the index number for Ca, which should be N(protein) + 1, is > > > actually N(protein) + N(solvent) + 1. Now the list of atoms in the > > > .xtc file is only N(protein) + N(Ca) + N(Cl) and the atom you're > > > trying to fetch brings you to a part of memory you're not allowed to > > > touch (index > N(protein) + N(Ca) + N(Cl)): a segmentation fault > > > > > > But since you did write out correctly, the solution is simple. First > > > make an index file to extract the matching set of atoms from the .tpr > > > file. Then write a matching reference structure. If you really need a > > > matching .tpr file, you can do it with tpbconv. Now with a matching > > > reference structure, you can do just what you want... > > > > > > Cheers, > > > > > > Tsjerk > > > > > > > > > > > > > > > On Thu, Apr 10, 2008 at 6:42 PM, Peggy Yao <[EMAIL PROTECTED]> > wrote: > > > > Thank you for your reply, Tsjerk! > > > > > > > > I used gmxcheck, and got exactly the same number of atoms in xtc > file as > > > > #proteinAtoms+#calciumAtoms+#chlorideAtom. > > > > > > > > I also checked my mdp file. It does have "xtc_grps = protein Ca Cl". > > > > > > > > In previous similar runs, I successfully wrote these atoms out. The > only > > > > difference is that, in previous runs, I added some Na+ ions too. At > the > > end > > > > of the .top file, I had: > > > > Protein_A 1 > > > > Na 15 > > > > Cl 12 > > > > SOL 7254 > > > > And, in mdp file, I had: xtc_grps = protein Ca Na Cl > > > > > > > > But this time, I didn't add any Na+ ion. After genion step, the end > of > > the > > > > .top file became: > > > > Protein_A 1 > > > > SOL 7280 > > > > Na 0 > > > > Cl 1 > > > > In mdp file, I had: xtc_grps = protein Ca Cl > > > > > > > > Will this difference cause the problem? How should I solve it? > Thanks a > > lot! > > > > > > > > Peggy > > > > > > > > > > > > > > > > On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar < > [EMAIL PROTECTED]> > > > > wrote: > > > > > > > > > Hi Peggy, > > > > > > > > > > I suspect that in your .mdp file you have a line > > >
Re: [gmx-users] Bad .tpr or .xtc files?
Thank you for the explanation! In fact, 2 Ca atoms are a part of the protein. They are in the PDB file passed to pdb2gmx. Water molecules are added after the protein atoms and the Ca atoms, as in the PDB file after genbox. So I suppose, in the .tpr file, atoms should be ordered as protein-Ca-water-Cl? If I still have to do what you suggested, could you kindly tell me: 1. what is an index file? 2. how to make an index file to extract the matching set of atoms from .tpr file? 3. how to write a matching reference structure? Thanks a lot! Peggy On Thu, Apr 10, 2008 at 11:52 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Peggy, > > The key thing is that there's a mismatch between your .tpr file and > your .xtc file. The first is used for the indexing and it may very > well be that there's stuff in between the protein and the calcium. > That way, the index number for Ca, which should be N(protein) + 1, is > actually N(protein) + N(solvent) + 1. Now the list of atoms in the > .xtc file is only N(protein) + N(Ca) + N(Cl) and the atom you're > trying to fetch brings you to a part of memory you're not allowed to > touch (index > N(protein) + N(Ca) + N(Cl)): a segmentation fault > > But since you did write out correctly, the solution is simple. First > make an index file to extract the matching set of atoms from the .tpr > file. Then write a matching reference structure. If you really need a > matching .tpr file, you can do it with tpbconv. Now with a matching > reference structure, you can do just what you want... > > Cheers, > > Tsjerk > > On Thu, Apr 10, 2008 at 6:42 PM, Peggy Yao <[EMAIL PROTECTED]> wrote: > > Thank you for your reply, Tsjerk! > > > > I used gmxcheck, and got exactly the same number of atoms in xtc file as > > #proteinAtoms+#calciumAtoms+#chlorideAtom. > > > > I also checked my mdp file. It does have "xtc_grps = protein Ca Cl". > > > > In previous similar runs, I successfully wrote these atoms out. The only > > difference is that, in previous runs, I added some Na+ ions too. At the > end > > of the .top file, I had: > > Protein_A 1 > > Na 15 > > Cl 12 > > SOL 7254 > > And, in mdp file, I had: xtc_grps = protein Ca Na Cl > > > > But this time, I didn't add any Na+ ion. After genion step, the end of > the > > .top file became: > > Protein_A 1 > > SOL 7280 > > Na 0 > > Cl 1 > > In mdp file, I had: xtc_grps = protein Ca Cl > > > > Will this difference cause the problem? How should I solve it? Thanks a > lot! > > > > Peggy > > > > > > > > On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> > > wrote: > > > > > Hi Peggy, > > > > > > I suspect that in your .mdp file you have a line > > > > > > xtc-grps = Protein > > > > > > This means that the xtc file will only contain those atoms which > > > gromacs reckognizes as amino acids, based on the list in the file > > > aminoacids.dat. Your .tpr file which is used to base the index on, > > > contains all atoms, including the Ca/Cl. You can easily check how many > > > atoms there are in your xtc file using gmxcheck and compare this to > > > the groups you see based on the .tpr as you've given. If you need the > > > calcium and chloride in the trajectory while you've only written > > > Protein, you'll have to redo the simulation, changing the xtc-grps > > > line in the .mdp, copy the file aminoacids.dat and add the ions to it > > > or use an index file when running grompp. Of course you can first have > > > a look at teh .trr file which contains all atoms by definition, but > > > that is usually written much less frequent. > > > > > > Cheers, > > > > > > Tsjerk > > > > > > > > > > > > > > > On Thu, Apr 10, 2008 at 8:27 AM, Peggy Yao <[EMAIL PROTECTED]> > wrote: > > > > Hi all, > > > > > > > > In my system, I have 1 protein, 2 calcium atoms, and 1 chloride > atom. > > When I > > > > used trjconv to write the protein out as PDB file, it worked fine. > > However, > > > > when I tried to write the calciums and chloride out using the same > > command > > > > (but selecting different group to write out), I got the following > fatal > > > > error: > > > > > > > > for calcium: > > > > Select group for output > > > > Opening library file /usr/share
Re: [gmx-users] Bad .tpr or .xtc files?
Thank you for your reply, Tsjerk! I used gmxcheck, and got exactly the same number of atoms in xtc file as #proteinAtoms+#calciumAtoms+#chlorideAtom. I also checked my mdp file. It does have "xtc_grps = protein Ca Cl". In previous similar runs, I successfully wrote these atoms out. The only difference is that, in previous runs, I added some Na+ ions too. At the end of the .top file, I had: Protein_A 1 Na 15 Cl 12 SOL 7254 And, in mdp file, I had: xtc_grps = protein Ca Na Cl But this time, I didn't add any Na+ ion. After genion step, the end of the .top file became: Protein_A 1 SOL 7280 Na 0 Cl 1 In mdp file, I had: xtc_grps = protein Ca Cl Will this difference cause the problem? How should I solve it? Thanks a lot! Peggy On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Peggy, > > I suspect that in your .mdp file you have a line > > xtc-grps = Protein > > This means that the xtc file will only contain those atoms which > gromacs reckognizes as amino acids, based on the list in the file > aminoacids.dat. Your .tpr file which is used to base the index on, > contains all atoms, including the Ca/Cl. You can easily check how many > atoms there are in your xtc file using gmxcheck and compare this to > the groups you see based on the .tpr as you've given. If you need the > calcium and chloride in the trajectory while you've only written > Protein, you'll have to redo the simulation, changing the xtc-grps > line in the .mdp, copy the file aminoacids.dat and add the ions to it > or use an index file when running grompp. Of course you can first have > a look at teh .trr file which contains all atoms by definition, but > that is usually written much less frequent. > > Cheers, > > Tsjerk > > On Thu, Apr 10, 2008 at 8:27 AM, Peggy Yao <[EMAIL PROTECTED]> wrote: > > Hi all, > > > > In my system, I have 1 protein, 2 calcium atoms, and 1 chloride atom. > When I > > used trjconv to write the protein out as PDB file, it worked fine. > However, > > when I tried to write the calciums and chloride out using the same > command > > (but selecting different group to write out), I got the following fatal > > error: > > > > for calcium: > > Select group for output > > Opening library file /usr/share/gromacs/top/aminoacids.dat > > Group 0 ( System) has 22737 elements > > Group 1 ( Protein) has 894 elements > > Group 2 ( Protein-H) has 707 elements > > Group 3 ( C-alpha) has89 elements > > Group 4 (Backbone) has 267 elements > > Group 5 ( MainChain) has 357 elements > > Group 6 (MainChain+Cb) has 440 elements > > Group 7 ( MainChain+H) has 447 elements > > Group 8 ( SideChain) has 447 elements > > Group 9 ( SideChain-H) has 350 elements > > Group10 ( Prot-Masses) has 894 elements > > Group11 ( Non-Protein) has 21843 elements > > Group12 ( Ca) has 2 elements > > Group13 ( SOL) has 21840 elements > > Group14 ( Cl) has 1 elements > > Group15 ( Other) has 21843 elements > > Select a group: 12 > > Selected 12: 'Ca' > > Reading frame 0 time0.000 > > Precision of traj.xtc is 0.001 (nm) > > Segmentation fault 3 time 150.000-> frame 3 time 150.000 > > > > for chloride: > > Select group for output > > Opening library file /usr/share/gromacs/top/aminoacids.dat > > Group 0 ( System) has 22737 elements > > Group 1 ( Protein) has 894 elements > > Group 2 ( Protein-H) has 707 elements > > Group 3 ( C-alpha) has89 elements > > Group 4 (Backbone) has 267 elements > > Group 5 ( MainChain) has 357 elements > > Group 6 (MainChain+Cb) has 440 elements > > Group 7 ( MainChain+H) has 447 elements > > Group 8 ( SideChain) has 447 elements > > Group 9 ( SideChain-H) has 350 elements > > Group10 ( Prot-Masses) has 894 elements > > Group11 ( Non-Protein) has 21843 elements > > Group12 ( Ca) has 2 elements > > Group13 ( SOL) has 21840 elements > > Group14 ( Cl) has 1 elements > > Group15 ( Other) has 21843 elements > > Select a group: 14 > > Selected 14: 'Cl' > > Reading frame 0 time0.000 > > Precision of traj.xtc is 0.001 (nm) > > --- > > Program trjconv, VERSION 3.3.2 > > Source code fil
[gmx-users] Bad .tpr or .xtc files?
Hi all, In my system, I have 1 protein, 2 calcium atoms, and 1 chloride atom. When I used trjconv to write the protein out as PDB file, it worked fine. However, when I tried to write the calciums and chloride out using the same command (but selecting different group to write out), I got the following fatal error: for calcium: Select group for output Opening library file /usr/share/gromacs/top/aminoacids.dat Group 0 ( System) has 22737 elements Group 1 ( Protein) has 894 elements Group 2 ( Protein-H) has 707 elements Group 3 ( C-alpha) has89 elements Group 4 (Backbone) has 267 elements Group 5 ( MainChain) has 357 elements Group 6 (MainChain+Cb) has 440 elements Group 7 ( MainChain+H) has 447 elements Group 8 ( SideChain) has 447 elements Group 9 ( SideChain-H) has 350 elements Group10 ( Prot-Masses) has 894 elements Group11 ( Non-Protein) has 21843 elements Group12 ( Ca) has 2 elements Group13 ( SOL) has 21840 elements Group14 ( Cl) has 1 elements Group15 ( Other) has 21843 elements Select a group: 12 Selected 12: 'Ca' Reading frame 0 time0.000 Precision of traj.xtc is 0.001 (nm) Segmentation fault 3 time 150.000-> frame 3 time 150.000 for chloride: Select group for output Opening library file /usr/share/gromacs/top/aminoacids.dat Group 0 ( System) has 22737 elements Group 1 ( Protein) has 894 elements Group 2 ( Protein-H) has 707 elements Group 3 ( C-alpha) has89 elements Group 4 (Backbone) has 267 elements Group 5 ( MainChain) has 357 elements Group 6 (MainChain+Cb) has 440 elements Group 7 ( MainChain+H) has 447 elements Group 8 ( SideChain) has 447 elements Group 9 ( SideChain-H) has 350 elements Group10 ( Prot-Masses) has 894 elements Group11 ( Non-Protein) has 21843 elements Group12 ( Ca) has 2 elements Group13 ( SOL) has 21840 elements Group14 ( Cl) has 1 elements Group15 ( Other) has 21843 elements Select a group: 14 Selected 14: 'Cl' Reading frame 0 time0.000 Precision of traj.xtc is 0.001 (nm) --- Program trjconv, VERSION 3.3.2 Source code file: gmx_trjconv.c, line: 994 Fatal error: Index[0] 22737 is larger than the number of atoms in the trajectory file (897) --- Does anybody know what might be wrong? Maybe the .tpr or .xtc files are not complete? Is there any way to check? Thanks! Peggy ___ 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] Help with energy minimizing protein in water box with CA2+
Dear Gromacs users,
Thanks for earlier help on this problem.
I have tried a number of approaches with varying results (all bad,
unfortunately). I am trying to add two CA2+ ions to my protein (1k9p), but
when I did this genion put the two CA2+ ions very close together and they
flew apart. Then I tried putting only one CA2+, thinking that it would stay
put. After I ran an energy minimization, the CA2+ ended up outside of the
box. Now I am really perplexed. What could be causing this behavior? One
thing I haven't tried yet is adding a few CL- ions to make the box neutral
.. somehow I don't feel this is the problem though since I've run
non-neutral analyses before without such disastrous consequences.
Could anyone give me some advice? I'm at my wit's end. I am attaching my
script below. Basically fws_ca.pdb is fine, but fws_b4ion.pdb has CA2+
outside of the water box. The water in the water box looks like ice cubes
in an ice cube tray, segregated into regular little mini-boxes. I presume
the latter is a numerical consequence of the CA2+ flying out of the box.
Many thanks for any help..
Peggy
pdb2gmx -ignh -ff gmx -f 1K9P.pdb -p fws.top -o fws.pdb
# add water
editconf -bt cubic -f fws.pdb -o fws.pdb -c -d 0.9
genbox -cp fws.pdb -cs spc216.gro -o fws_b4em.pdb -p fws.top
# energy minimization
grompp -f minim.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
echo "check 2"
mdrun -v -s fws_em.tpr -o fws_em.trr -c fws_b4ca.pdb -g em.log -e em.edr
# add calcium
grompp -f minim.mdp -c fws_b4ca.pdb -p fws.top -o fws_ca.tpr
echo "12" | genion -s fws_ca.tpr -o fws_ca.pdb -pname Ca -np 1 -g fws_ca.log
-norandom
awk '{if ($1 == "SOL") {print "Ca 1"; print "SOL 7280"} else {print $0;}}'
fws.top > temp.top
mv temp.top fws.top
# energy minimization
grompp -f minim.mdp -c fws_ca.pdb -p fws.top -o fws_em2.tpr
mdrun -v -s fws_em2.tpr -o fws_em2.trr -c fws_b4ion.pdb -g em.log -e em.edr
___
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] Why so many energy minimization and position restrained simulation steps?
Hi, I am new to Gromacs. I am following this tutorial: http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html. My question is: why it has multiple steps of energy minimization and position restrained simulation? Is that a common practice? What's the key difference among these steps? Thanks! Peggy ___ 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] How to specify .mdp file for position restrained simulation?
Hi, How to specify the .mdp file in order to run position restrained simulation? From the examples I found on the internet, it seems that the only difference between the .mdp file for position restrained simulation and the one for actual MD simulation is the simulation time -- the position restrained simulation is much shorter. Is this observation true in general? If yes, usually, how long is enough for the position restrained simulation? If not, how to specify the .mdp file for position restrained simulation then? Thanks a lot! Peggy ___ 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 add calcium ions at desired position?
Thank all of you for the suggestions! I then ran the procedures described at (http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html), where it adds water before energy minimization, and it also has position restraint step. But when I came to the step: grompp -f dyna/pr1_SOLV.mdp -po X_pr1.mdp -c X_em3.gro -r X_em3.gro -t X_em3.trr -n X.ndx -p X.top -o X_pr1.tpr mdrun -v -deffnm X_pr1 I got the following error: --- Program mdrun, VERSION 3.3.2 Source code file: network.c, line: 437 Routine should not have been called: gmx_sumi --- I used exactly the same .mdp files as in the tutorial, with the only modification in pr1.mdp to set T-coupling to "Protein Non-Protein". Does anybody know what might be the problem? Thanks! Peggy On Nov 19, 2007 3:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > Quoting liang <[EMAIL PROTECTED]>: > > > > Never couple solvent and ions separately. Check out: > > > > > http://wiki.gromacs.org/index.php/Thermostats > > > > > Try tc-grps = Protein Non-protein > > > > excuse me, if the system includes lipid bilayer, how should i set the > > tc-prgs? > > Protein + Lipids + Sol and Ion? > > or Protein + Non-protein ? > > I think either would work, but I've personally used protein, lipids, solvent + > ions. As long as you're not coupling a very small amount of atoms/ions to its > own bath then you should avoid problems. > > -Justin > > > > > thanks > > > > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ 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] How to add calcium ions at desired position?
Hi all, I would like to simulate a protein with calcium ions at the calcium binding sties. I cannot use genion to add calcium ions because genion put the ions randomly. Is there any conventional way to do this? The only way I could think of is the following: 1. Add the calcium ions in the protein PDB input file as HETATM with residue name CA2+. 2. pdb2gmx -f protein_ca.pdb -p protein_ca.top -o protein_ca.gro 3. In protein_ca.top, the last portions is ; Compound#mols Protein_A1 Protein_B1 Change the last line (Protien_B ...) to: CA2+ 2 4. Minimize energy, and add water. 5. In md.mdp, set: tc-grps = protein sol CA2+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 6. grompp -f md.mdp -c protein_ca_water.gro -p protein_ca.top -o md.tpr 7. mdrun -s md.tpr -o protein.trr -x protein.xtc -c protein.gro However, after several MD steps, I got the following fatal error: --- Program mdrun, VERSION 3.3.2 Source code file: nsgrid.c, line: 220 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. --- Why it is so? How should I do it? I am a new user of Gromacs, and I've been struggling on this issue for an entire day already. I will appreciate it very much if someone could help me. Thanks a lot! Peggy ___ 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
