AMBER Archive (2007)

Subject: Re: AMBER: some input problem

From: David A. Case (case_at_scripps.edu)
Date: Sun Dec 09 2007 - 11:09:51 CST

On Sun, Dec 09, 2007, Urszula Uciechowska wrote:
>
> initial minimisation
> &cntrl
> imin = 1,
> maxcyc = 500,
> ncyc = 250,
> ntb = 0,
> ntr = 1,
> ntpr = 10,
> igb = 2,
> cut = 12
> /
> Restrain the protein backbone atoms
> 10.0
> RES 1-255_at_CA,C,A
> END
> END

You are mixing up the two forms of input for atom selection. The newer one
(which is easier to use) is described in the atommask section of the manual.
You probably want something like this:

   restraintmask=':1-255_at_CA,C', restraint_wt=10.0,

This is roughly what you wrote above in intent. I'm not sure if you have any
atoms named "A" in your structure, or exactly which atoms you wish to
restrain, however.

With this method, you don't need any input lines after the namelist section.

...good luck....dac

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