AMBER Archive (2006)

Subject: AMBER: New (small) Topology without solvent from previous one (big) with solvent

From: j j (fantvamp_at_gmail.com)
Date: Thu Jul 13 2006 - 05:50:55 CDT

Sorry, where I said 'where' I wanted to say 'when'

I would like to ask if there is anyway to get new topology file
where solvent (or masked residues or atoms from ptraj stripped )
from previous one which had included all these residues.
The purpose of this questions is about ptraj use, where I'm getting
average structures for masked residues stripping the rest.
The output I want is a restart file and also a pdb.
What I'm doing by now is loading the new pdb into leap, and then
another new topology file, but this new just have essential solute
information. In this way I need the parm data file, when all
was contained in the previous 'big' topology file.
Summing up :
Is there anyway to delete information from a 'big' topology file to get a
new one which correspond to the
coord files obtained in the same flow of ptraj, or , not by using leap &
parm files?
Thank you very much,
 JJ

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