excluded interactions (NNB) in psf file for FEP simulations

From: Aman (sangha11_at_gmail.com)
Date: Tue Aug 27 2013 - 10:16:38 CDT

I am having trouble minimizing a system prepared using Mutate Plugin for
FEP simulation. The system I have is a tetramer and I have mutated one
amino acid in all the four protein chains using Mutate Plugin. I
alchemified the psf file after adding water box and ions to the system. All
the Non-bonded interactions in the psf file are there from all the 4
proteins. But i am having trouble minimizing the system due to Low Global
exclusion error!

I followed a previous thread (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11487.html ) on
namd-l forum about this topic where it has been discussed that alchemify
does not support mutation for more than two groups. So in my case, does
that mean that i can not perform free energy perturbation on amino acid in
all four proteins? For monomer, I do not see any problems and it works fine.

Does anyone know if the code has been updated and alchemify supports more
than two groups now?

Thanks in advance,

Aman Sangha

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