Hi Алексей, We have no use for your PDB files anyway :) In order not to loose the phospho from your tyrosine, you want to start out with trjconv -pbc whole. To obtain what you desire, you probably want to give the following a good read: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions There are some tips there on the use of trjconv.
Cheers, Tsjerk On Tue, Mar 1, 2011 at 10:09 AM, Алексей Раевский <[email protected]> wrote: > Hi, I want to ask you for help. I've got a trr file after 5 ns > simulation on the desktop 2 quad. The object is a complex of protein > and ligand (the itp file for ligand was prepeared by server), in > adition, I made some changes in rtp, atp, bon.itp databases to obtain > a phosphorylated tyrosine. When I used a trjconv command to convert > trr to xtc or to pdb I found that my comlex in the first frame was > devided between several cells (the result of the standard command). > So I tried different variants to gather everything in one cell: > > 1)trjconv -f sys1md.trr -s sys1md.tpr -o dyrk_ehb1.pdb -sep -n > sys1em1.ndx -b 1 -e 100 -skip 10 -pbc nojump > > 2) trjconv -f sys1md.trr -s sys1md.tpr -o dyrk_ehb2.pdb -sep -n > sys1em1.ndx -b 1 -e 100 -skip 10 -center -pbc mol -ur compact > > > I've even tried to follow one variant by another. But the results are the > same. > As you see I can loose my ligand or phosphate from tyrosine. Index > file, I used in the command, contains a new group "complex", which > includes atoms of protein without hydrogenes, ligand with hydrogenes. > I've got a one more result, but I can't find this file. In those case > I loosed some other aminoacids, but ligand and phosphate are Ok. > > Thank you > > (P.S. I sent a letter with attached sample pdb files, but moderators > didn't passed it) > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
