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

From: case <>
Date: Mon, 2 Jul 2012 21:17:55 -0400

On Mon, Jul 02, 2012, Ilyas Yildirim wrote:
> My question is what this (bad) prmtop file will do on the pressure
> calculations. In both, (bad) prmtop and (right) prmtop files, I have
> exactly the same ATOMS_PER_MOLECULE sections. Does that mean the pressure
> calculations will be the same, as well? Or during the pressure
> calculations, some other sections in prmtop files (combined with
> ATOMS_PER_MOLECULE) are used? Thanks.

My guess is that the pressure errors will be completely negligible. Assuming
you have lots of water molecules around your biomolecules, the water is the
dominant contribution to the pressure. You could do a short re-run of some
segment to check this.


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Received on Mon Jul 02 2012 - 18:30:02 PDT
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