Subject: CCL: Free Energy Perturbation

From: Bjørn Olav Brandsdal <[email-masked]>
Date: Fri, 20 Feb 1998 09:35:12 +0100

Hello,
I am trying to perform a free energy perturbation/simulation of a 
protein-inhibitor complex using the academic version of CHARMM. I have had 
some problems when trying to create a proper input file for a mutation of 
an amino acid to another in the inhibitor. In the testcases distributed 
along with CHARMM, there was an example of an input file for perturbation, 
and I have used the punit file for this exapmle. However, it ony calculates 
the first line of this file, that it lambda 0.0 to 0.05, then the program 
terminates normally. This is the same for all mutations I have done when 
the number of atoms in the two residues to be mutated are the same. When 
the number of atoms are different in the lambda 0 and 1 state, dummy atoms 
must be defined, and there does not seem to an easy way of doing this in 
CHARMM. So I was wondering if anyone has an exapmle of an input file for 
free energy perturbation for CHARMM, and if somebody could tell me of how 
to add dummy atoms.

Best regards,
Bjoern O. Brandsdal

Bjoern Olav Brandsdal
Department of Chemistry
University of Tromsoe
9037 Tromsoe, Norway

Phone: +47-776-44063
Fax:     +47-776-44765

E-mail: [email-masked]