Re: [AMBER] ATP minimization

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Wed, 22 Feb 2012 19:22:38 +0100

Dear Sangita Kachhap,

> Thanks Francois for Quick reply.
>
> But there is parameter only for monophosphate not triphosphate is
> available on link you have suggested.

there are mono, di, tri, tetra etc ;-)
see XYP (Adenosine monophosphate, Adenosine diphosphate, Adenosine
triphosphate, ...)

run xleap -f http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff

and you will get more than 200 biochemical cofactors

regards, Francois


>>> I am minimizing ATP binding protein having bound ATP. I have
>>> generated parameter for ATP.
>>> protein structure getting minimized but ATP purine getting
>>> distorted. Can anyone
>>> please help me to solve this.
>>
>> You might compare your parameters with these available in R.E.DD.B.
>> See http://q4md-forcefieldtools.org/REDDB/projects/F-90/
>> & http://q4md-forcefieldtools.org/REDDB/projects/F-91/
>>
>> regards, Francois



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Received on Wed Feb 22 2012 - 10:30:03 PST