Re: [AMBER] Problem with bonds in NAB

From: David A Case <>
Date: Thu, 3 Nov 2016 07:44:35 -0400

On Wed, Nov 02, 2016, Vladislav Sláma wrote:
> I’m trying to use Amber14 for calculation of normal modes of fluorographene
> sheet. For this purpose I’m using NAB, but it seams to me that NAB does not
> include all bonds which are written in parameter file (prmtop). When I
> minimize structure with sander I receive a right (expected) structure.
> However if I load the same molecule and parameters into NAB and minimize the
> molecule I obtain completely different structure than from minimization with
> sander.

On the surface, this seems pretty unlikely. Have you compared the energies
from a single-point calculation in sander and NAB (using the same prmtop

Note that you are doing a much more thorough minimization in NAB than
in sander (since you are doing a full Newton Raphson minimization to a very
small rms force in NAB). It is possible that this is the origin of what you
see. Take the output from the NAB minimization and use is as input to sander:
do you get the same energies?


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Received on Thu Nov 03 2016 - 05:00:03 PDT
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