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
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
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Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Tue Nov 15 2011 - 10:30:03 PST
