[gmx-users] creating trajectory with ligand close to the protein

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Feb 24 07:33:45 CET 2008

Hi David,

If you use a structure file (.gro/.pdb) which corresponds to the
starting structure and has the protein and ligand in the right place,
you can do it with trjconv -pbc nojump.



On Sun, Feb 24, 2008 at 4:47 AM, David Osguthorpe
<David.Osguthorpe at uchsc.edu> wrote:
> On Sun, Feb 24, 2008 at 01:35:51PM +1100, Mark Abraham wrote:
>  > >
>  > >Ive been using trjconv but it seems to be failing for a case where the
>  > >protein switches
>  > >image in the trajectory but the ligand does not.
>  >
>  > Check out trjconv -h, and if none of the options works, please describe
>  > why they're failing :-)
>  >
>  Ive been using -pbc cluster with an index file of protein and ligand which has worked for other systems
>  (which is the closest Ive got to the algorithm I described previously although none of trjconvs options
>  or any other gromacs utility seem to implement the algorithm I described - if you could suggest which
>  utility/option is the closest to the above algorithm Id be very grateful)
>  but for a particular system it went into an infinite loop printing out
>  COM:    0.911     1.167     5.420  iter = 1
>  etc. (with iter going up forever) forever and a day.
>  Dumping coordinates before and after the step where this occurred and inspection by molecular graphics
>  showed that the ligand coordinates were similar but the protein coordinates were very different
>  - which I assume means the protein shifted to a different periodic image - hence the comment.
>  David
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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

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