Hi Jason and Brian,
thanks much for the advice!
much appreciated,
-Dave
On Tue, Nov 15, 2011 at 6:55 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Just to add on to what Brian said, the bellymask specifies the atoms that
> can move, NOT that you want to hold fixed. You can use positional
> restraints, too, which will have basically the same effect with strong
> force constant (see ntr=1 in the manual).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Nov 15, 2011, at 1:17 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > Hi Dave,
> >
> > I think you can accomplish your goal with the belly module (look up
> > "ibelly" and "bellymask" in the manual). That would just involve
> > additions/changes to the sander input file hardcoded into Jason's script.
> > I should mention that belly is an older module that is to be eschewed in
> > most cases (especially dynamics), but I think it's ok here. I'm sure a
> > more veteran AMBER user will chime in if I am mistaken.
> >
> > Regards,
> > Brian
> >
> > On Tue, Nov 15, 2011 at 9:51 AM, David Condon <dec986.gmail.com> wrote:
> >
> >> Hello,
> >>
> >> I found a script to do a relaxed potential energy surface scan on
> >> http://archive.ambermd.org/201002/0249.html, by Jason Swails.
> >>
> >> However, only only want to relax 6 atoms out of 30, because the tleap
> file
> >> I used loaded the PDB with incorrect bond lengths. I only have to do
> this
> >> minimization once before running the PES, then I can modify his
> >> minimization script to do a single point energy calculation. Gaussian
> has
> >> something close called Opt(ReadFreeze).
> >>
> >> How can I only minimize certain atoms from the starting PDB?
> >>
> >> Thanks for your time,
> >> -Dave
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Wright-Rieman Hall
> 101
> > Graduate Program in Chemical Physics : 610 Taylor Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 16 2011 - 07:00:04 PST
