AMBER Archive (2008)

Subject: Re: AMBER: query regarding energy minimization

Date: Mon Apr 28 2008 - 09:26:25 CDT

Since you are new to AMBER, the best thing to do is to understand the AMBER
protocols by following the DNA tutorial (written by Ross Taylor) step by step.
This will be a very good starting point to get you going.

Raviprasad Aduri

Quoting Anamika Awasthi <>:

> 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
> Thanks in advance
> --
> Anamika Awasthi

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