[gmx-users] g_hbond routine
Dear gromacs users, in the Gromacs manual pages (version 4.5.3 page 211) there are the criteria to have an Hbond. r 0.35 nm, where r is the Donor-Acceptor distance alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle in the Manual page for g_hbond (version 4.5.3 page 275) it is written Hydrogen bonds are determined based on cutoffs for the angle Acceptor - Donor - Hydrogen (zero is extended) and the distance Hydrogen - Acceptor and even in the file that exits by using the option -dist the xaxis label is Hydrogen - Acceptor Distance (nm) but I think this is the Donor-Acceptor distance because it seems too big to be the Hydrogen-Acceptor distance. Which distance is it? Thank you very much, Velia -- 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] [Fwd: problem after genion]
Sorry. I understood the problem! I included ions.it twice. Thanks, Velia Messaggio Originale Oggetto: problem after genion Data: Fri, 19 Jun 2009 11:21:05 +0200 (CEST) Da: Velia Minicozzi velia.minico...@roma2.infn.it A: gmx-users@gromacs.org Dear users, I used genion to neutrilize my system with two Na+ ions. Now with my new .gro and .top file and with a minimization (mdp) input file I try to make a .tpr file with grompp in order to minimize my structure. When I run grompp I get an error Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 967 Fatal error: moleculetype CU2+ is redefined but I have any CU2+ atom! I have a Zn2+, so I really don't understand what it does mean. Thanks in advance, Velia * Velia Minicozzi Department of Physics University of Rome Tor Vergata Via della Ricerca Scientifica, 1 00133 Rome - Italy tel. +39 06 72594554 fax. +39 06 2023507 http://biophys.roma2.infn.it/ * ___ 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] problem after genion
Dear users, I used genion to neutrilize my system with two Na+ ions. Now with my new .gro and .top file and with a minimization (mdp) input file I try to make a .tpr file with grompp in order to minimize my structure. When I run grompp I get an error Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 967 Fatal error: moleculetype CU2+ is redefined but I have any CU2+ atom! I have a Zn2+, so I really don't understand what it does mean. Thanks in advance, Velia * Velia Minicozzi Department of Physics University of Rome Tor Vergata Via della Ricerca Scientifica, 1 00133 Rome - Italy tel. +39 06 72594554 fax. +39 06 2023507 http://biophys.roma2.infn.it/ * ___ 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] Charmm_gromacs
Hi, I am trying to run gromacs using CHARMM force field. I downloaded charmm_gromacs.tar.gz file and I followed the instruction, that housed in readme-charmmed-gromacs. I runned the command: pdb2gmx -ter -f filename.pdb -o filename.gro -p filename.top, using as input file the *.gro file of the example, but the following error message is coming: Program pdb2gmx, VERSION 3.3.1 Source code file: ter_db.c, line: 85 Fatal error: Reading Termini Database: expected 3 items of atom data in stead of 1 on line N NH314.0027-0.3000 Thank you for reply. Velia -- Velia Minicozzi, Physics Dept., University of Rome Tor Vergata Via della Ricerca Scientifica, 1 - 00133 Roma tel: +39 0672594554 - fax: +39 06 2023507 ___ 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] Charmm_gromacs
I think we have understood the problem...if it's not true I will write again... Thanks. Velia Minicozzi On Wed, June 11, 2008 12:12 pm, Velia Minicozzi said: Hi, I am trying to run gromacs using CHARMM force field. I downloaded charmm_gromacs.tar.gz file and I followed the instruction, that housed in readme-charmmed-gromacs. I runned the command: pdb2gmx -ter -f filename.pdb -o filename.gro -p filename.top, using as input file the *.gro file of the example, but the following error message is coming: Program pdb2gmx, VERSION 3.3.1 Source code file: ter_db.c, line: 85 Fatal error: Reading Termini Database: expected 3 items of atom data in stead of 1 on line N NH314.0027-0.3000 Thank you for reply. Velia -- Velia Minicozzi, Physics Dept., University of Rome Tor Vergata Via della Ricerca Scientifica, 1 - 00133 Roma tel: +39 0672594554 - fax: +39 06 2023507 ___ 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 * Velia Minicozzi Department of Physics University of Rome Tor Vergata Via della Ricerca Scientifica, 1 00133 Rome - Italy tel. +39 06 72594554 fax. +39 06 2023507 http://biophys.roma2.infn.it/ * ___ 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] interchain bond
Thank you Xavier, but I still have problems because when I use merge, pdb2gmx doesn't want that the second peptide has NH3+ and COO- as terminals and doesn't understand if I use -ter when I am using -merge, so doesn't create the top file. What do you exactly mean for the numbering of atoms is important? I tried in two ways: 1. Each peptide starts form one 2. The second peptide numbering starts from the end of the first in both cases I have the same results and none of them works. Cheers and thank you, Velia Xavier Periole ha scritto: On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal is labeled with a third identifier, and I modified the ffoplsaabon.itp file inserting this bond and the specbond.dat file. Having 3 chains I have 3 different itp files and one top file in which all of the itp are called. Unfortunately in none of the itp files nor in the top file there is any reference to this bond I created, and after some time of MD simulation two of the atoms bound to the metal fly away even if I use constraints on all bonds. You have to use the merge option of pdb2gmx, it will generate one topology of the two peptides and the metal. Then you can add the bond within this topology file. The numbering of the atoms is important. If you create a chemical bond between two topologies (peptide-metal) this will not work. I guess I didn't create those bonds correctly. How should I do? Any help is welcome! Best, Velia ___ 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 - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ 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] interchain bond
Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal is labeled with a third identifier, and I modified the ffoplsaabon.itp file inserting this bond and the specbond.dat file. Having 3 chains I have 3 different itp files and one top file in which all of the itp are called. Unfortunately in none of the itp files nor in the top file there is any reference to this bond I created, and after some time of MD simulation two of the atoms bound to the metal fly away even if I use constraints on all bonds. I guess I didn't create those bonds correctly. How should I do? Any help is welcome! Best, Velia ___ 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
