[AMBER] keeping parts of a protein virtually frozen in MD with pmemd

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Wed, 29 Aug 2012 14:28:53 -0400

Hi everyone,

I have a protein of 992 residues solvated in a 15A box. I want to run MD
with two loops in the protein virtually frozen. As sander is very slow for
this big a system I am using pmemd. pmemd doesn't support 'bellymask' to
keep the loops without moving so I am using the group specifications. How
big a force constant would be sufficient? Would something like 200
kcalmol-1A-2 be suffice to keep the loops virtually frozen? or would this
cause the structure to break down as other connecting parts are moving
while these two loops are fixed? Your advice is highly appreciated

Thank you
Sajeewa Dewage
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Received on Wed Aug 29 2012 - 11:30:02 PDT
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