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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Aug 06 2012 - 02:36:47 CDT

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Hello:
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)?

Thanks

francesco pietra

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