[gmx-users] trjconv problem

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 1 10:47:19 CET 2011

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:
There are some tips there on the use of trjconv.



On Tue, Mar 1, 2011 at 10:09 AM, Алексей Раевский <rayevsky85 at gmail.com> 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)
> --
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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

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