Alchemical protein transformation with a group of (non proteic) atoms bound to two amino acids

From: Francesco Pietra (
Date: Mon Aug 06 2012 - 02:36:47 CDT

I start from no experience with alchemical free energy methods.

I wonder whether - in the context of NAMD FEP, or other a_t - the
transformation of a protein can be studies where a small group of (non
proteic) atoms becomes bound to two different aa. Each aa loses one H
from N or O from a side chain during the process.

I have already simulated the unbound and bound states with PARM7 in
NAMD-CUDA and plan to explore Felmerino's recent suggestion that, by
arranging the input Cartesian coordinates in PDB format, FEP could
probably be carried out with PARM7/NAMD.

It is not entirely clear to me if a_t theories allow this case, and,
if it does, how the PDB file could be arranged (a single set of lamda
0,1 for both)?


francesco pietra

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:53 CST