Re: [AMBER-Developers] TER card issue with ambpdb

From: Jason Swails <>
Date: Mon, 2 Jul 2012 18:12:21 -0400

On Mon, Jul 2, 2012 at 5:04 PM, Ilyas Yildirim

> > Now, if you make a link between metal1 and chain1, you get a new molecule
> > (made up of the atoms in chain1 plus metal1) that are not contiguous
> > in atom sequence. In this case, LEaP doesn't complain, but creates an
> > incorrect prmtop file (with a bad ATOMS_PER_MOLECULE section.) The
> > ambpdb program uses this information to create (bad) TER cards; but
> > the sander/pmemd programs also use this (bad) information in computing
> > pressures. So, the prmtop file has to be fixed.
> Thanks for the information Dave. How bad would this (bad) prmtop affect
> the computed pressures in sander/pmemd calculations? I have done a bunch
> of calculations with (bad) prmtop and wonder if I should throw everything
> out. Thanks.

Before throwing everything out, there is a simple test to see if anything
is blatantly *wrong*. A simple test is your_prmtop <<EOF
setMolecules True
outparm test.prmtop

This should dump test.prmtop with a "correct" ATOMS_PER_MOLECULE section
(and SOLVENT_POINTERS). If the ordering is messed up, you'll see a message
like "Molecule atoms are not contiguous!". Otherwise, compare the two
prmtops (ignoring whitespace). If

diff -w your_prmtop test.prmtop

returns differences, it's worth inspecting them.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Jul 02 2012 - 15:30:03 PDT
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