Re: [AMBER] ATP minimization

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Sun, 26 Feb 2012 22:46:57 +0530 (IST)

Hello Francois

I have not able run this command

Shall I use link you have given in command line:

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


or I have to run command:
        xleap -f script1.ff



I have tried both fist one didnt run

When try second

Its showing

> POP = loadmol2 ./tripos1.mol2
Could not open file ./tripos1.mol2: No such file or directory





> 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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>


Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH

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सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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Received on Sun Feb 26 2012 - 09:30:03 PST
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