Re: [AMBER] Minimization of only certain atoms

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 15 Nov 2011 18:55:26 -0500

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
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> 
> 
> 
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Received on Tue Nov 15 2011 - 16:00:10 PST