On Tue, Apr 24, 2018, Tousif Hossen wrote:
>
> 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,
it's simpler to leave iresid at it's default value of 0
> r1=0.00000, r2=2.00000, r3=2.00000, r4=99.00000,
> rk2=6.0, rk3=6.0,
> igr1=??????
igr1 would be list of atoms in residues 1-7, e.g.
igr1=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16, ....
> igr2=????
igr2 is the list of atoms in residue 8.
> grnam1(1)=??????,
> grnam2(1)=??????,
Above are not needed.
...hope this helps....dac
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Received on Tue Apr 24 2018 - 05:30:03 PDT
