Re: AMBER: restraining atoms

From: Thomas Cheatham III <>
Date: Mon, 14 May 2007 11:27:01 -0600 (Mountain Daylight Time)

> In my simulation , although I am able t restrain atoms but it seems to me as
> if only first group of atoms is bein restrained and not all. can somebody
> clear my doubt whether only first group of atoms, following thr restrain
> command gets fixed or all?
> I have attached my input script and i feel as if only 10-20 atoms are
> restrained and not 25,26,28-38 atoms.

The output file (mdout) lists what atoms are being restrained; please
refer to this to see if the atoms are being selected appropriately. Also
note that an alternative syntax (if the above is not being parsed
correctly) would be

restraintmask = '.10-20 | .25 | .26 | .28-38'

Finally, the atoms will not be "fixed" or constrained but restrained, i.e.
there will be force to move them back to the desired position...

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Received on Wed May 16 2007 - 06:07:19 PDT
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