[gmx-users] setup problem
tsjerkw at gmail.com
Wed Mar 7 17:52:13 CET 2007
Probably, the .tpr file you used for trjconv -pbc nojump already had
the ligand jumped. In that case, you will find all frames consistently
having a shift between the ligand and the protein. Make sure you use a
reference which has the ligand in place (the .pdb or .gro file you
used to set up the system for example).
Oh, and do read about periodic boundary conditions.
On 3/7/07, merc mertens <merc.mertens at gmx.net> wrote:
> thank you for your suggestions. actually i tried all -pbc options, but neither did help. but i think i found the solution in an old posting from ka feenstra. there he writes that due to efficiency (iirc) at least one atom of each part of the system has to be in the rectangular waterbox. therefore the translation i think. so rotating my protein such that the ligand is at least partly immersed in the solvent helped to solve the problem. actually i could have found the solution in the manual, chapter 3, as well. seems to be worth reading that in-depth ;)
> -------- Original-Nachricht --------
> Datum: Wed, 07 Mar 2007 11:20:22 +1100
> Von: Mark Abraham <Mark.Abraham at anu.edu.au>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] setup problem
> > merc mertens wrote:
> > > hello,
> > >
> > > i have got a problem with my simulation setup. i prepare a protein with
> > two ligands in a dodecahedral box. after the setup the ligands are situated
> > in the active site of the protein all right. when i look at the structure
> > after em one of the ligands is now outside the protein in the solvent. if i
> > generate symmetry mates the ligand is perfectly at its typical position in
> > the active site of the next symmetry related molecule. yet the flag "-pbc
> > nojump" in trjconv does not produce a whole molecule!! therefore it seems
> > that the ligand is translated during the em step. when i look at the
> > structure before em i see that the ligand is outside the solventbox (but inside
> > the dodecahedral box!!!) and translated inside the solventbox after em.
> > unfortunately i have no idea how to solve this problem except to make the box so
> > huge, that calculation becomes too time consuming, as the protein is a
> > tetramer with nearly 1500 residues.
> > Have you tried the trjconv option that puts the COM of each molecule (or
> > residue, I forget) inside the box?
> > Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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