Re: [gmx-users] suggest small revision to genbox
genbox works fine for me. i use 3.3.1 version. it works fine with and without script. but i don't understand how will u get rid of backup files in the permanent directory from whatever u have mentioned, because gromacs creates the output topology in the same location where it reads the input topology from. so temperory directory thing will work only if u make an link of top file from permanent directory and use this linked version as input, then move the new top from temp to permanent directory. bharat On Fri, 11 May 2007, David Mobley wrote: All, I'm trying to write some wrappers to set up a project using standard gromacs tools. Anyway, it looks to me like genbox is not handling its path names correctly. In particular, here's what I did: - Make temporary directory in which to run genbox - Move to temporary directory, run genbox (reading input files from permanent directory; writing input files to permanent directory) - Change back to starting directory; delete temporary directory When I do this, I get a blank output topology file in my permanent directory. It appears what's going on is that the file temp.top is written into my temporary directory, but never moved into the permanent directory; I suspect genbox is not handling the absolute/relative path issue correctly here? I can work around, but this is just a bit annoying -- when I script it, I end up with a bunch of #temp.top.1# etc files in my working directory if I use editconf in the normal way, which is why I was using the temporary directory thing to begin with. Thanks, David ___ 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
Re: [gmx-users] suggest small revision to genbox
David Mobley wrote: All, I'm trying to write some wrappers to set up a project using standard gromacs tools. Anyway, it looks to me like genbox is not handling its path names correctly. In particular, here's what I did: - Make temporary directory in which to run genbox - Move to temporary directory, run genbox (reading input files from permanent directory; writing input files to permanent directory) - Change back to starting directory; delete temporary directory When I do this, I get a blank output topology file in my permanent directory. It appears what's going on is that the file temp.top is written into my temporary directory, but never moved into the permanent directory; I suspect genbox is not handling the absolute/relative path issue correctly here? I can work around, but this is just a bit annoying -- when I script it, I end up with a bunch of #temp.top.1# etc files in my working directory if I use editconf in the normal way, which is why I was using the temporary directory thing to begin with. Hi David, plz submit a bugzilla with all input and scripts. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error while running MD in DMSO!
Dear All, I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it is running fine but while running in DMSO. After running genbox i am having problem in running grompp for energy minimization. Error which i got is given below. Cleaning up temporary file gromppkkHvWC Fatal error: Atomtype 'SD' not found! Please, anyone let me know why it is happening when i had used the dmso.gro and dmso.itp files which is available by default to top folder. Thanks in advance. With Warm Regards Anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant ___ 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] Error while running grompp for em (MD) in Urea
Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below. I have added masses of all the atoms of urea in atommass.dat file, but still getting the same error. Please help me, where does am i making the mistakes. processing coordinates... Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) (more than 20 non-matching atom names) WARNING 3 [file base.top, line 808]: 6150 non-matching atom names atom names from base.top will be used atom names from after_sol.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 945 # G96BONDS: 128 # ANGLES: 1215 # G96ANGLES: 190 # PDIHS: 1134 # IDIHS: 485 # LJ14: 1242 # SETTLE: 2050 ERROR 4 [file base.top, line 808]: atom C1 (Res UREA-11) has mass 0 ERROR 5 [file base.top, line 808]: atom O2 (Res UREA-11) has mass 0 ERROR 6 [file base.top, line 808]: atom N3 (Res UREA-11) has mass 0 ERROR 7 [file base.top, line 808]: atom H4 (Res UREA-11) has mass 0 ERROR 8 [file base.top, line 808]: atom H5 (Res UREA-11) has mass 0 ERROR 9 [file base.top, line 808]: atom N6 (Res UREA-11) has mass 0 ERROR 10 [file base.top, line 808]: atom H7 (Res UREA-11) has mass 0 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- I'm An Oakman (Pulp Fiction) Thanks in advance. With Warm Regards anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) - Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) - Web:http://chemanil.googlepages.com/ -- Education is a progressive discovery of our ignorance - Will Durant Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: CNT Potassium doping with GROMACS (George Abadir) 2. Re: Cannot find fftw3f (Mark Abraham) 3. Re: suggest small revision to genbox (bharat v. adkar) 4. Re: suggest small revision to genbox (David van der Spoel) 5. Error while running MD in DMSO! (Anil Kumar) -- Message: 1 Date: Fri, 11 May 2007 18:52:43 -0700 From: George Abadir [EMAIL PROTECTED] Subject: Re: [gmx-users] CNT Potassium doping with GROMACS To: [EMAIL PROTECTED],Discussion list for GROMACS users
RE: [gmx-users] problem with freeze-group : Large VCM(Berk Hess)
Hi Berk, Thanks a lot for your reply. According to your suggestion, I did not remove the cmm for the WHOLE molecule i.e I used 'cmm-mode=None'for the entire system. (Did you mean that I should have removed the restriction only for freeze-group or for whole system?) But now I have two problems: 1) the simulation is now going for longer time but finally again crashes. 2) I freezed the mainchain because I did not want the mainchain move at all and I wanted the only side-chain move. But , when I am visualising the trajectory in VMD, I am finding that whole molecule is tumbling including the main-chain i.e the whole molecule is changing its position. As ususal, I did not use pressure coupling . Do you think that the movement of whole molecule is expected during freeze group simulation? should I modify something else in my parameter file? I am again giving the .mdp file. --- Berk Hess [EMAIL PROTECTED] wrote: From: jagannath mondal [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] problem with freeze-group : Large VCM Date: Fri, 11 May 2007 00:19:53 +0100 (BST) Hi Gromacs user, I am a gromacs beginner struggling with freeze-group simulation. I was trying to simulate a beta-peptide(un-natural peptide ) by relaxing only the side-chains but I am getting error regarding large VCM and The system has only 1 peptide (14-residue ) and No solvent. So, for this purpose , I generated a freeze-group which contains all the main-chain atoms. Initially I was using pressure-coupling and it was giving error in simulation. Later I found many discussion on this freeze-group simulation in user-archive and manual and accordingly I did not use pressure-coupling in my simulation and before the simulation, I minimised my peptide using steep integrator and then with the minimised structure I tried a MD run. But after 40 ps, the mdrun crashes with complaint about nsgrid and large VCM: You should not remove com motion when using freeze groups, since the com is no longer free to move. We should let grompp print a warning for this. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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 Office firewalls, cyber cafes, college labs, don't allow you to download CHAT? Click here: http://in.messenger.yahoo.com/webmessengerpromo.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
Re: [gmx-users] Error while running MD in DMSO!
Anil Kumar wrote: Dear All, I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it is running fine but while running in DMSO. After running genbox i am having problem in running grompp for energy minimization. Error which i got is given below. Cleaning up temporary file gromppkkHvWC Fatal error: Atomtype 'SD' not found! Please, anyone let me know why it is happening when i had used the dmso.gro and dmso.itp files which is available by default to top folder. They have to match the force field you're using, and the structure file you're using. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error while running grompp for em (MD) in Urea
Anil Kumar wrote: Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below. I have added masses of all the atoms of urea in atommass.dat file, but still getting the same error. This file isn't used for making topologies. Please help me, where does am i making the mistakes. processing coordinates... Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Well, if these don't match you're doing something wrongly, but I can't tell what. double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 945 # G96BONDS: 128 # ANGLES: 1215 # G96ANGLES: 190 # PDIHS: 1134 # IDIHS: 485 # LJ14: 1242 # SETTLE: 2050 ERROR 4 [file base.top, line 808]: atom C1 (Res UREA-11) has mass 0 ERROR 5 [file base.top, line 808]: atom O2 (Res UREA-11) has mass 0 ERROR 6 [file base.top, line 808]: atom N3 (Res UREA-11) has mass 0 ERROR 7 [file base.top, line 808]: atom H4 (Res UREA-11) has mass 0 ERROR 8 [file base.top, line 808]: atom H5 (Res UREA-11) has mass 0 ERROR 9 [file base.top, line 808]: atom N6 (Res UREA-11) has mass 0 ERROR 10 [file base.top, line 808]: atom H7 (Res UREA-11) has mass 0 Your force field's .rtp file needs entries for these atoms, probably. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Parameterizing a force field (Mark Abraham)
Lee-Ping wrote: Thank you both for the response! I looked at the -j option in mdrun, but it looks like that has about as much documentation as ffscan (i.e. none at all). I also fruitlessly checked the mailing list archives for the past year and a half; there are some questions about ffscan, but none of which contained instructions on how to run it. The next step is to look inside the gromacs source code, but there are a lot of different files and I'm not sure as to which pieces of source code describe how the input files are parsed. If you could tell me which files to look at, I would appreciate it a lot. Thanks again! Mostly, files that parse files end in io.c Specifically: 1) What piece of code do I look at to see how mdrun parses the wham.gct file (turned on by the -j switch)? Don't know. Start with src/kernel/mdrun.c and see what it calls to parse this file. 2) Which file describes how ffscan parses its inputs? Start with src/kernel/ffscan.c and see what it calls :-) Also: If ffscan performs a grid scan, is it really able to fit 100+ parameters in a reasonable period of time (couple of hours)? Would a numerical optimization procedure for the parameters be a possible improvement over this? ffscan doesn't do a fit, per se, it just does a grid scan and reports suitable values (see man ffscan). It'd have to be heaps faster than your alternative scripts calling grompp and mdrun to do your series of single point energy evaluations. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CNT Potassium doping with GROMACS
George Abadir wrote: Hi, I want to make a simulation of CNT in an environment of potassium atoms to see how they will be adsorbed on the CNT surface (this is a way of doping carbon nanotubes). I built a .pdb file with a CNT and some potassium atoms with random coordinates around the nanotube. When I run x2top to have my topology file, I get the error:No forcefield type for atom K with 0 bond. The problem is that the atoms of potassium should indeed be not bonded to anything at the beginning of the simulation. Does anybody have a way to describe such a system and avoid this error? Thank you very much in advance, first make a topology for the CNT with x2top, then manually add the potassium (chapter 5). Regards, George ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat
Nicolas Sapay wrote: Hello, I'm trying to create a topology file of a system made of a protein homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA, SOD, ZN2). The system has been initially built with CHARMM and all hydrogens are already included. I use an implementation of CHARMM for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is to check if it is easy to use pdb files previously built with CHARMM with my implementation of the CHARMM ff in Gromacs. That is why I use a difficult system with dimer, cys-cys bridges, zinc finger, etc... I use the following command to create the topology file: pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff charmm27 I have a first problem with the 2 zinc fingers. pdb2gmx find the 2 cys-cys bridges without trouble but failed with the bonds between the ZN2s and the CYSs. I have modified specbond.dat as following: CYS SG 1 ZN2 ZN 4 0.2 CYSZZN2 with ZN2, the residue name of the Zn ion and CYSZ, the residue name for coordinated CYSs. Both residues are defined in ffcharmm27.rtp. However, I haven't found documentation on how to modify specbond.dat. So, I have guessed what the different parameters mean and I'm pretty sure to have done something wrong. Can someone correct my specbond definition and tell me what the different parameters signify? the 0.2 is the bondlength and currently there is a hard toloerance of 10% on that. Check the special bond matrix to see what happens. The second problem comes when pdb2gmx try to add hydrogens. It crashes with the following message : WARNING: atom CD1 not found in residue 84 while adding atom --- Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CD1 not found in residue TRP84 while adding hydrogens --- is your ffcharm27.hdb file correct? since you already have hydrogens you probably don't need to add them. However, the CD1 atom is indeed present in the pdb file and TRP residues upstream to TRP84 are perfectly treated. Additionally HD1 atoms is properly defined in the .hdb file. I have tried to create the .top file on a single monomer and it works perfectly. I have also tried to merge the homodimer using the -merge option of pdb2gmx but it crashes again on the second TRP84... Any suggestion are welcomed! Thanks Nicolas -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
