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

From: Ilyas Yildirim <>
Date: Mon, 2 Jul 2012 16:04:15 -0500 (CDT)

> 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.


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Received on Mon Jul 02 2012 - 14:30:02 PDT
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