AMBER Archive (2008)

Subject: Re: AMBER: query regarding energy minimization

From: D.Usharani (usha_at_ipc.iisc.ernet.in)
Date: Tue Apr 29 2008 - 00:20:29 CDT

Hello anamika,

If your trying to do an explicit solvent simulation then you have to
minimize your solvent first. If your system is DNA then please try doing
the AMBER 8 Tutorial − DNA (poly−A−poly−T)or
Amber8 introductory tutorial in case if it is protein, your doubts will be
clarified.

ntr=1

to read the restraint

Group input for restrained atoms
> 100.0
restraint wt in kcal/mol

> RES 1 155
Now coming to the term RES means here residue and the numbers are
concerned to the residues that you want to fix during the simulation. So
first you will write all the residue number of protein and DNA atoms to be
fixed during minimization.
> END
> END

regards
usha

> Dear Friends,
> I prepared input for energy minimization using LEAP, but not
> getting, how should I do energy minimization.
> I found in tutorial that first I should do energy minimization of
> only solvent and then after I should do for whole system and there is also
> mention that I should prepare one minimization file as input for SANDER,
> but
> the problem is this I am not getting the meaning of all the terms, Altough
> I
> tried to understand, but still fail to understand the what is the criteria
> to give RES 1 155
> imin=1, maxcyc=200,
> ntpr=5,
> ntr=1,
> &end
> Group input for restrained atoms
> 100.0
> RES 1 155
> END
> END
>
> Thanks in advance
> --
> Anamika Awasthi
>
> --
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>

*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
D.Usharani
c/o Prof E.D.Jemmis
Inorganic and PhysicalChemistry
Indian Institute of Science
Bangalore -560012
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* 

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