Thank you very much Sir, it's running now.
i have one further confusion for negative distance scanning.
like
r1=-99.00000, r2=-2.00000, r3=-2.00000, r4=0.00000,
is it correct?
> 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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--
Tousif Hossen
Research Scholar
Department of Chemistry
IIT GUWAHATI
INDIA
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Received on Wed Apr 25 2018 - 07:30:02 PDT
