AMBER Archive (2008)

Subject: RE: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 22 2008 - 10:54:51 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Pavan G
Sent: Thursday, May 22, 2008 8:38 AM
To: amber_at_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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