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 - 05:00:02 PDT
