Hi Pavan,
I believe that imin=5 is what you require - see page 24 of the AMBER 10
manual. Note you will need to produce a protein only prmtop file as well.
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Pavan G
Sent: Thursday, May 22, 2008 8:38 AM
To: amber.scripps.edu
Subject: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a
system
Hello All,
I have a few nanoseconds of data with a protein in solvent and would like to
calculate the bond/angle/dihedral/improper/vdw for the protein alone at
every time step. I generated a protein-only subset of the trajectory and a
topology file as well. Is there a code to read through the trajectory and
give the energies as the output? It should be fairly easy to write one but I
was wondering if this has already been done.
Thanks.
Pavan
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Received on Sun May 25 2008 - 06:07:32 PDT
