Hi Rebeca, In the GMX data directory ($GMXDATA) there's a file aminoacids.dat listing what should be recognized as amino acids. Either edit the file and add HIE (also incrementing the counter at the top line) or make a local copy of the file in the directory where you need it and edit that.
Cheers, Tsjerk On Tue, Aug 12, 2008 at 5:47 PM, Rebeca García Fandiño <[EMAIL PROTECTED]> wrote: > Hello, > I am trying to simulate a protein that has 2 chains (in a membrane, but the > problem is in the protein). One of the chains of the protein has 416 > residues and the other 421. I want to simulate it using the amber force > field, so I have prepared the topology for each one of them and then > converted them with amb2gmx.pl. > > When I do grompp of the complete system I can see that it is only > considering 821 residues of the protein, and they should be 837!!: > > Opening library file > /gpfs/projects/ub51/ub51077/GROMACS-4.0-DEV/share/gromacs/top/aminoacids.dat > There are: 157455 OTHER residues > There are: 821 PROTEIN residues > There are: 0 DNA residues > > The problem is that the program considers residues HIE out of the protein > (histidines): > > 0 System : 716705 atoms > 1 Protein : 12658 atoms > 2 Protein-H : 6344 atoms > 3 C-alpha : 821 atoms > 4 Backbone : 2463 atoms > 5 MainChain : 3286 atoms > 6 MainChain+Cb : 4038 atoms > 7 MainChain+H : 4072 atoms > 8 SideChain : 8586 atoms > 9 SideChain-H : 3058 atoms > 10 Prot-Masses : 12658 atoms > 11 Non-Protein : 704047 atoms > 12 HIE : 272 atoms > 13 dop : 238464 atoms > 14 SOL : 464400 atoms > 15 Na : 467 atoms > 16 Cl : 444 atoms > 17 Other : 704047 atoms > > > I have tried to use both chains together and repeating the same, but the > result is the same. > > What could I do? Anybody knows why there is a problem with HIE? > > Thank you very much in advance, > > Rebeca Garcia Fandiño > Parc Cientific de Barcelona > > > > > ________________________________ > ¡Es tiempo de inaugurar tu piscina! Entra en Eventos e invita a todos tus > amigos, crea paneles de discusión y sube las fotos más divertidas Eventos > _______________________________________________ > gmx-users mailing list gmx-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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-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
