Re: Generalized Born and OPLS potential

From: David A. Case <case_at_scripps.edu>
Date: Mon 5 Aug 2002 08:51:30 -0700

On Sat, Aug 03, 2002, Soonmin Jang wrote:
>
> As I know, one can incorporate OPLS force field in Amber7 in principle.
> Then, my question is this. Is it possible to have the GB(generalized Born)
> with this OPLS force field ? If so, how ? If not, is there any way that I
> can add the GB potential with OPLS force field ?

You could run GB with OPLS, but the GB parameters have not been optimized
for this (especially not tested at all for united-atom carbons), so I don't
think the results would be very good.

Also, please remember that the OPLS force field files in the Amber
distribution are about 10 years old. The newer OPLS/AA force field parameters
have not (yet?) been coverted to Amber.

...dac 


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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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From jcanon_at_yaw.org 6 Aug 2002 14:50:53 -0000
Message-id: <20020806145053.19929.qmail.yaw.org>
Date: 6 Aug 2002 14:50:53 -0000
From: Jim <jcanon_at_yaw.org>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: "number of processors must be a power of two"
In-Reply-to: <200208030805.g7385R617609.protege.snu.ac.kr>
When running amber 7 using the PBS I receive the following error:
number of processors must be a power of 2, and no greater than 128:
            3
[0] MPI Abort by user Aborting program !
[0] Aborting program!
Does sander require the number of processors to be a power of 2? Is 
this perhaps a mpich or beowulf limitation? Thank you.
Jim
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Received on Mon Aug 05 2002 - 08:51:30 PDT
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