Alchemical with parm7 ff

From: Francesco Pietra (
Date: Wed Jul 11 2012 - 03:39:30 CDT


I would like to know whether the following alchemical simulation (TI,
FEP, ABF, or other) can be carried out with NAMD under parm7 ff.

I.e., I am interested in a protein that reacts with a drug, inserting
a piece of the drug between two aas. The non-covalent complex of the
protein with the drug is stable for the 20ns trajectory carried out
with NAMD/parm7, and I assume there would be no major problem in
carrying out alchemicals for that. I would also like to carry out
alchemicals with the covalently reacted protein plus the other moiety
of the drug, which remains non-covalently bound at the active site. To
this concern, I remember vaguely that parm7 has limitations to this
regard (more than one species).

Finally, I am at CPU-GTX680-GPU. Is 2.9 with CUDA able to use the GPU
for such calculations?

I regret for having missed any post related to my questions.


francesco pietra

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