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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 26 2012 - 09:30:03 PST
