AMBER Archive (2008)

Subject: RE: AMBER: query regarding energy minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 29 2008 - 01:16:11 CDT

Hi Anamika,

 

There is no requirement for you to minimize the solvent first and then the
solute. In most cases, since minimization is done just to remove bad
contacts prior to MD then it is fine to just do a few hundred steps of
minimization on everything at once. However it can't hurt to be more
cautious and minimize the solvent then the solute.

 

As for your query about the input. RES 1 155 means restrain residues 1 to
155 with a harmonic restraint of 100.0 Kcal/mol/A2 to the structure
specified by the -ref flag on the sander executable line.

 

See http://www.ambermd.org/tutorials/basic/tutorial1/index.htm

 

For an introduction to MD and the initial minimization etc. You should also
note that the format you describe below is the "old style" group input. You
can now use a newer input format which would be:

 

ntr=1,

restraint_wt=100.0, restraint_mask=':1-155;,

 

which would accomplish the same thing.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Anamika Awasthi
Sent: Monday, April 28, 2008 6:22 AM
To: amber_at_scripps.edu
Subject: AMBER: query regarding energy minimization

 

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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