On Fri, 2014-05-30 at 11:46 -0400, Lara rajam wrote:
> Dear amber
>
> I am trying to use the amber in namd
>
> I have already got the links through [ AMBER group]and they are useful
>
> I am not understanding the restrain for equilibration in namd ( fixing the
> solute molecule), How one should do it ?
I believe you need a PDB file for this, and the occupancy column is used
to mark atoms to restrain, and I _think_ VMD has a utility that will
create this file for you.
> suggestions regarding this will help me in understanding
This mailing list is probably the wrong place for questions about
running NAMD (most people here -- and all of the frequent responders --
use Amber mostly, if not exclusively). You would have better luck
answering your questions by looking in the NAMD user manual and
consulting with the NAMD mailing list instead. This task is
sufficiently common that I would be surprised if their manual did not
tell you how to do this.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 30 2014 - 09:00:05 PDT
