Re: [gmx-users] B-factor
- Original Message - From: Tsjerk Wassenaar tsje...@gmail.com Date: Friday, July 2, 2010 14:10 Subject: Re: [gmx-users] B-factor To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 The last column is the occupancy (1.00) and temperature factor numbers concatenated. You can fix the symptoms by editing the file by hand so that these numbers occupy the right columns - see the PDB format. This illustrates buggy behaviour from GROMACS. src/tools/gmx_rmsf.c probably needs to call set_pdb_wide_format(TRUE) before write_sto_conf_indexed(). Please file a bugzilla (see GROMACS webpage). I disagree. The PDB file is fixed width, and the format for the b-factor field is %6.2f. This means that the above line is a proper PDB ATOM definition. Using the Gromacs pdb_wide_format generates a PDB file that may not be compatible with other programs. I would argue True. I misread what was happening with the pdbform variable and leapt to a conclusion. The observed GROMACS behaviour now looks correct. I don't recall what symptoms the OP had, but presumably they were related to the function of the correctly-formatted file with some (other) software that assumes space-delimited PDB fields. Mark though that Gromacs should at least warn when trying to write numbers larger than 999.99 to the b-factor/occupancy field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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 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] GBSA calculations
- Original Message -
From: Hassan Shallal hshal...@pacific.edu
Date: Friday, July 2, 2010 17:40
Subject: [gmx-users] GBSA calculations
To: gmx-users@gromacs.org
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Dear Gromacs users, I am running some simulations of ligand protein
systems using GBSA option for the implicit solvent. In an MM/GBSA model,
there is this equation: G(molecule) = G(solvations) + Egas -
TS(solute)... G(molecule) is the total free energy of solute
G(solvations) is the solvation free energy Egas is the moelcular
mechanical energy of the molecule summing up the electrostatic interactions,
van der Waal contributions and the internal strain energy TS(solute) is
the sum of TS(trans), TS(rot), and TS(vib) How can derive such a
calculation from the input of my Gromacs simulation... I looked in the
mailing list, there were a couple of inquiries about this issues without
reponses. I know those calculations can be run through Amber which I don't
have an access to, so first question is, can I execute those calculations
from the Gromacs simulation output files like from the .edr for example? and
if yes, any hint or reference on how to do this would be greatly
appreciated...
Until the release of GROMACS 4.5, this will not be available. After that
release, it will surely be in the manual :-)
Mark
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[gmx-users] mk_angndx
Hi all, I am trying to make a PCA analysis of an protein md trajectory in dihedral space. Anyway I don't really understand how to use mk_angndx . When I run this command: mk_angndx -s ../foo.tpr -n dangle.ndx -type ryckaert-bellemans it seems that the resulting index file contains all the dihedrals in the tpr structure file grouped by the force constant of the first Ryckaert-Bellemans coefficient, but I want only the phi-psi dihedrals. Is there a way of doing this? Thanks, Andrei Dr. Andrei Neamtu, PhD, Lecturer Dept. of Physiology Gr. T. Popa Iasi University of Medicine and Pharmacy http://www.umfiasi.ro/ str. Universitatii nr. 16 IASI, Jud. Iasi ROMANIA -- -- 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] contact map
Hi gromacs users after simulation of protein-ligand, in analysis section, how to obtain contact map for protein-ligand? thanks in advance. -- atila -- 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] contact map
atila petrosian wrote: Hi gromacs users after simulation of protein-ligand, in analysis section, how to obtain contact map for protein-ligand? Try g_mdmat. -Justin thanks in advance. -- atila -- 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 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] Re: gmx-users Digest, Vol 75, Issue 18
Quoting gmx-users-requ...@gromacs.org: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: g_principal: memory corruption (David van der Spoel) -- Message: 1 Date: Sat, 03 Jul 2010 09:36:58 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] g_principal: memory corruption To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c2ee89a.2070...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2010-07-03 02.40, kulleperuma.kulleper...@utoronto.ca wrote: Hi all, I am using Gromacs-4.0.5 g_principal for a system with a protein of 132 resiudes, ~450 octane molecules and ~9000 water molecules, as below, g_principal -f pos_Rep.xtc -s em.tpr -n index.ndx (Protein was the selected group ). I get the follwing message soon after I selected Protein Reading frame 0 time 0.000 *** glibc detected *** g_principal: malloc(): memory corruption: 0x0646c250 *** === Backtrace: = /lib64/libc.so.6[0x2b4788cd24ac] /lib64/libc.so.6(__libc_calloc+0xc0)[0x2b4788cd3ce0] g_principal[0x41071c] g_principal[0x471aff] g_principal[0x472237] g_principal[0x410539] g_principal[0x40251f] g_principal[0x402139] /lib64/libc.so.6(__libc_start_main+0xf4)[0x2b4788c7d974] g_principal[0x402079] === Memory map: . This error didn't occur and ran smoothly when .gro file was selected for -f flag, but failed even for a shorter trajectory file. What is the way around for this problem Thank you in advance! Please submit a bugzilla with a short trajectory (since it crashes at time 0 one frame is enough). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 75, Issue 18 * Thank you David and sorry for the late reply, The problem is fixed. It's my mistake, I have been using a xtc file from a position restrained equilibration, where the protein was fixed -- 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] residue names in rtp file and their parameters
Dear gmx-users, I am trying to derive parameters of novel molecules consistent with ffG53a6. To get a feel of the parameterization, I am reading ffG53a6.rtp file. Let me please ask some questions about ffG53a6.rtp. My questions are as follows: 1) What molecules do residue names in rtp file stand for, respectively? Could you let me know the related literatures? 2) There are some residues which are not listed in the original paper of ffG53a5/6 (e.g. ATP, HEME). How were these parameters derived? Is it consistent with the method described in the paper, i.e. are charges fitted to reproduce the corresponding experimental value? With respect to ffgmx.rtp, I found the correspondences between molecule full names and residue names at http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks . However ffG53a6.rtp seems to have been updated in some respects. Best regards, Shuntaro. -- 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
