On Tue, Sep 6, 2016 at 11:37 AM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> Hello,
>
> I want to calculate the pairwise energy decomposition between the ligand
> and every residue within 3 Ang. So I have 2 questions in this regard.
>
> 1) how to find ONLY the PROTEIN residues that are within 3 Ang. from the
> ligand?
>
You can use the "mask" command in cpptraj to get this information by using
the distance selection criteria. There is some documentation in ParmEd
about the distance syntax:
http://parmed.github.io/ParmEd/html/amber.html#distance-based-selections
2) how to calculate the pairwise energy decomposition using only pairs that
> contain the ligand in order to speed up the calculations?
>
Sander does not support this to my knowledge. As far as I've been able to
tell, it can only accept one set of residues as input. However, you'd need
two selections to implement this feature (all interactions between members
of group 1 with members of group 2).
>
> For 1) I tried to extract the last frame of the trajectory as rst file like
> this:
>
> cpptraj -p complex.prmtop
> > trajin complex.prod_GB.nc lastframe
> > trajout last_frm.rst
> > go
> > quit
>
Just use the "mask" command in cpptraj directly. That eliminates the need
to use ambmask and can work over every frame in a trajectory.
HTH,
Jason
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 06 2016 - 10:00:03 PDT
