Dear amber users,
Currently I am using amber12. I am trying to
calculate PMF (potential mean force) between a
host-guest system in water. I am using
beta-cyclodextrin as host molecule. it
contains 1-7 residues. My guest is a small
organic molecule, only one residue, named as
8. I want to calculate PMF between COMs
(center of mass) of the host-guest.
But I am facing problem to create restraints file.
Example of my disang.2 file
&rst
iat=-1,-1,
iresid=1,
r1=0.00000, r2=2.00000, r3=2.00000, r4=99.00000,
rk2=6.0, rk3=6.0,
igr1=??????
igr2=????
grnam1(1)=??????,
grnam2(1)=??????,
I am unable to mention proper ‘igr’ and ‘granam’ selection for center of
mass scan of host-guest system.
I want to scan from -10Å to 10Å.
Thank you in advance.
--
Tousif Hossen
Research Scholar
Department of Chemistry
IIT GUWAHATI
INDIA
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Received on Tue Apr 24 2018 - 04:30:02 PDT
