Re: AMBER: umbrella sampling

From: David A. Case <>
Date: Thu, 29 Jul 2004 11:19:13 -0700

On Thu, Jul 29, 2004, tang kwa wrote:
> Now I am trying to calculate PMF using umbrella
> sampling. I got the problem in the history file. It
> showed the torsion angle is zero in all steps.

> -----RST file -----------
> # 1 MOL CHIr: (1 MOL O1)-(1 MOL C7)-(2 MOL O1)-(2 MOL C7) 0.0 0.0
> &rst iat = 43, 21, 43, 21,

You have to specify four different atom numbers for a torsion; but you have
"43,21,43,21" which is not a correct set of atoms. It looks like you want two
atoms in one chain/residue and two in another; you will have to figure out
what actual atom numbers are, and put them in there.

I don't know if you tried to use an auxiliary program to prepare the RST
file, but for a single torsion it is generally easiest just to create this
by hand.

....good luck...dac
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Received on Thu Jul 29 2004 - 20:53:00 PDT
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