Re: constraint + restraint

From: David A. Case <>
Date: Thu, 19 Jun 2003 08:39:44 -0700

On Thu, Jun 19, 2003, Jose Ramon Blas wrote:

> I am trying to run a MD simulation of a protein + waterCAP (many of the
> residues of my protein are constrained by ibelly). In the same run, I
> would like to restraint the distance between 2 atoms. (I use an
> harmonic term as usually). When I build this mixed input file the output
> gives 0.000 for all the energy terms.
> Is this mixture somehow forbidden in sander?? If allowed, what should be
> the order of the 2 parts in the sander input file?

The group commands for identifying the belly go at the end of the file,
after the &rst commands that define the distance restraints.

Getting zero for everything implies some deeper problem than just the
wrong order of things in the input. But you gave so little information
in your post that it is not possible to be of much help. At a minimum, we
would need to know what the input file looks like.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Thu Jun 19 2003 - 16:53:00 PDT
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