Subject: Free Energy Pert Scripts in CHARMM

From: "Kirby, Robert" <[email-masked]>
Date: Thu, 25 Jul 96 08:41:00 PDT

CCL,
 I am looking for example scripts which do Free Energy Perturbation   
Calculations using CHARMM. I have a couple of short ones from MSI but   
they do not cover the real situation of a molecule inside a protein   
generated in QUANTA and submitted to a CHARMM FEP calculation by a CHARMM   
script. If anyone has one of these lying around could I get a copy of it   
at your convenience.
Thank-you
  Robert A. Kirby
  BioChem Therapeutiques Inc.
  275 Armand-Frappier Blvd.
  Laval, Quebec,
  H7V 4A7
  #514-978-7914
  fax 514-978-7777
  [email-masked]  

From [email-masked] Jul 27 11:13:31 1996
Date: Wed, 10 Jul 1996 01:21:48 +0200
From: [email-masked]
To: [email-masked]
Subject: M: SADDLE
Status: RO
Content-Length: 1385

First, the SADDLE command does not give an optimized geometry of the TS -- only
an approximate geometry.  The "best" TS approximation must be refined using the
TS keyword, or NLLSQ, or some combination (perhaps in several steps), followed
by a FORCE calculation to assure you are at a TS (one -ve root to the Hessian),
and ideally followed by reaction coordinate calculations (IRC=1 and IRC=-1) to
generate the product and starting material.  Only through all this work can you
assure you have a TS for the reaction you are interested in.  This applies to
all TS, incidentally, whether you generate them by the SADDLE command or by
guessing.

Since your results are so spectacularly strange, it seems most likely that your
starting geometry for the separate pieces is indigestible.  I would do some
minimization in Mopac on the starting side before trying the saddle calculation.
I expect there are several "reasonable" geometries for this, and you might have
to try several before you get it right.

Given a "reasonable" starting geometry, you might try running the calculation in
AMPAC, if you have access to the program.  I believe the algorithm for locating
TS is different from that used in Mopac, but the two programs should give
otherwise very similar results (with minor modification, the AMPAC output can be
transferred to Mopac as well).  I think the keyword is CHAIN.

sb