preparing a dimeric protein for NAMD

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Dec 22 2005 - 21:28:21 CST

We have a dimer protein we're working with, and we're wondering whether
psfgen can cope with having the corresponding residues in both monomers
having the same resid , or do we have to renumber the 2nd monomer?

The pdb file from which we start [built by genomics types from an homology
model] starts with residue 26. Could that be a problem? At the very right of
each line is a field CHA for every atom in monomer 1 & CHB inr monomer 2,
but the field right after the atom type, which should contain A or B is
empty. [That matters to some viewers]. Should I populate it with As & Bs as
appropriate, or doesn't it matter to psfgen?

[We thought we'd gotten through the process with the initial pdb file as is,
but the protein sort of uncoils during MD. The other thing that's different
from our previous projects is that this protein has a lot of charged
residues, so needs to have counterions added. We're trying to figure out
where things went wrong & these two differences are our current focus].

Thanks!
Irene Newhouse
U. of Hawaii

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