Thank you Jason! How about restricting the selection to protein residues
only? Is it possible to include non-standard residues like phosphorylated
serines or threonines?
On 6 September 2016 at 18:37, Jason Swails <jason.swails.gmail.com> wrote:
> 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
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>
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Sep 06 2016 - 11:00:02 PDT
