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 list [email protected] >>>> 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 list [email protected] >> 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 list [email protected] > 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 list [email protected] 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
