Re: [AMBER] PBC error. Amber force field in NAMD

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Tue, 25 Sep 2018 13:34:28 +0000

Hi,


I guess this is more a question for the NAMD mailing list.

Nonetheless, the easiest way to do it is to use VMD to calculate the dimensions of your box as you would if you had instead prepared a pdb/psf pair of files for NAMD using the Charmm ff:


After loading your amber files in vmd. in the vmd tcl/tk console type:

set sel [atomselect top "all"]

measure minmax $sel

 -> will return {x1 y1 z1} {x2 y2 z2}

measure center $sel

-> will return x0 y0 z0


calculate x3=x2-x1, y3=y2-y1 and z3=z2-z1


then in your configuration file, since you have a rectangular box:


cellBasisVector1 x3 0 0
cellBasisVector1 0 y3 0
cellBasisVector1 0 0 z3
cellOrigin x0 y0 z0


Hope this helps,


Eric 


--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
________________________________
From: M RCC <mkr3j2c1.gmail.com>
Sent: 25 September 2018 12:34
To: amber.ambermd.org
Subject: [AMBER] PBC error. Amber force field in NAMD
Dear Amber users,
I want to use amber force field in NAMD. I have prepared the topology
(.prmtop) and coordinate (.inpcrd) files in tleap. I want to use this
topology in NAMD. HOW I can set Periodic cell vectors in .namd
configuration file.
while setting COM of protein as cell origin the box breaks in minimization.
Mine is a rectangular box with protein on one corner(for SMD constant
velocity pulling).
I want to set the following values in namd configuration file.
cellBasisVector1 *x1 y1 z1*,
cellBasisVector1 *x2 y2 z2*,
cellBasisVector1 *x3 y3 z3*
cellOrigin x y z
And the information I have
from .prmtop file
*%FLAG
BOX_DIMENSIONS
%FORMAT(5E16.8)
  9.00000000E+01  8.85883700E+01  8.84811760E+01  2.08344945E+02*
 and from leap.log file
Box:
   enclosing:  -45.96 -33.88 -96.75   43.62 36.38 -25.03
   sized:                  82.04 94.12 31.25
   edge:        128.00
Resolution:      1.00 Angstrom.
>From this information how i can get information for using in .namd
configuration file?
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Received on Tue Sep 25 2018 - 07:00:04 PDT
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