Re: [gmx-users] interchain bond
On Wed, January 16, 2008 10:40 pm, Xavier Periole said: > On Wed, 16 Jan 2008 22:29:31 +0100 (CET) > "Velia Minicozzi" <[EMAIL PROTECTED]> wrote: >> Hi Xavier, >> >> I think it works I just deleted the 3 H at the N-terminus of the second >> chain and when I used merge in pdb2gmx it worked! >> Thanks a lot! > > Cool. > > What I meant with the atom numbers is that now you can open your > gro file and look for the atom numbers to bound and go to the itp > file and add a bond (in the [ bond ]section) using these atom numbers. > Previously grompp would have attributed then to the same molecule. > Now they should be bound. > Yes I have done all this and added a bond in the bond section. > You can check the tpr file using gmxdump -s topol.tpr I will check tomorrow! Thank you very much! I didn't find many hints on the manual! The user group is really useful! > > > >> Velia >> >> On Tue, January 15, 2008 8:50 pm, Xavier Periole said: >>> 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 >>> - >>> >> >> >> * >> 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 > > - > 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 > * 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 PRO
Re: [gmx-users] interchain bond
On Wed, 16 Jan 2008 22:29:31 +0100 (CET) "Velia Minicozzi" <[EMAIL PROTECTED]> wrote: Hi Xavier, I think it works I just deleted the 3 H at the N-terminus of the second chain and when I used merge in pdb2gmx it worked! Thanks a lot! Cool. What I meant with the atom numbers is that now you can open your gro file and look for the atom numbers to bound and go to the itp file and add a bond (in the [ bond ]section) using these atom numbers. Previously grompp would have attributed then to the same molecule. Now they should be bound. You can check the tpr file using gmxdump -s topol.tpr Velia On Tue, January 15, 2008 8:50 pm, Xavier Periole said: 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 - * 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 - 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
Re: [gmx-users] interchain bond
Hi Xavier, I think it works I just deleted the 3 H at the N-terminus of the second chain and when I used merge in pdb2gmx it worked! Thanks a lot! Velia On Tue, January 15, 2008 8:50 pm, Xavier Periole said: > 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 > - > * 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
Re: [gmx-users] interchain bond
Xavier Periole wrote: 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. Maybe you want to create a bond of type 6. Such bonds will not be constrained with LINCS but restrain your metal ions to the peptides with a "real" harmonic potential... Cheers, Jochen 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 . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ 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
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
