[gmx-users] ligand falling out of active site during EM
tsjerkw at gmail.com
Wed May 10 09:31:13 CEST 2006
Maybe as a note for any interested but unaware. In gromacs, the middle of
the box is always the middle of the *rectangular* box defined by the first
three numbers in the last line of the .gro file.
On 5/9/06, Anton Feenstra <feenstra at few.vu.nl> wrote:
> Diane Fournier wrote:
> > Thank you !
> > I think the problem was indeed with building the box, because I redid
> > the whole sequence on my drug-enzyme system (building the box with
> > editconf, putting the water with genbox, and then writing my .tpr
> > file with grompp) and ran the same (test) position restraint md run,
> > and this time, the ligand was inside. Will try minimisation again.
> For the record: you have almost certainly had problems with PBC. mdrun
> will always place molecules 'in the box' (see manual). If your complex
> happens to be on the box edge, one molecule may end up at a different
> side of the box.
> If, instead, your complex was in the middle of the box, as probably
> happend during your second setup sequence, pbc will not affect it, at
> least not during EM when molecules tend not to move much.
> Note, that for different box shapes, the 'middle of the box' may not be
> what you expect.
> * NOTE: New Affiliation, Phone & Fax numbers (below) *
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
> | | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" (RHCP) |
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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