[AMBER] Problem with bonds in NAB

From: Vladislav Sláma <slama.karlov.mff.cuni.cz>
Date: Wed, 02 Nov 2016 16:39:12 +0100


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. This structure
looks like if some pairs of atoms were not treated as bonded. I
checked the prmtop file and it is correct (all bonds should be written
there). I would like to ask you if it is possible to add bonds between
two atoms in molecule or how to set NAB calculation correctly to get
the same results as with sander?
I would like to use comparison of normal mode analysis from forcefield
and normal mode analysis from quantum chemistry calculation for
fitting of FF parameters for small fluorographene sheet and then
finally use these parameters for normal mode calculation of large
fluorographene sheet with defects.
I’m using Amber14 with AmberTools15 with gaff forcefield and different
atom types for carbons and fluorines near the sheet borders and inside
the sheet. All input files are included in the attachment.

Thank you in advance for your help.

Kind regards,

Vladislav Slama

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Received on Wed Nov 02 2016 - 09:00:02 PDT
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