AMBER Archive (2008)

Subject: Re: AMBER: query regarding energy minimization

From: Deepangi Pandit (dnp5_at_njit.edu)
Date: Mon Apr 28 2008 - 09:39:39 CDT

Hi Anamika,
I also started using AMBER just months back. I feel the best thing is
to follow tutorials as mentioned earlier and refer to the manual of
AMBER which can be obtained from the website below.

http://amber.scripps.edu/

AMBER 9 Manual is below

http://amber.scripps.edu/doc9/amber9.pdf

All the best,
Deepa

On 4/28/08, Anamika Awasthi <aawasthi28_at_gmail.com> wrote:
> 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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