Re: Internal Restraints in Sander Problem

From: Bill Ross <ross_at_cgl.ucsf.edu>
Date: Wed 11 Jul 2001 15:40:55 -0700 (PDT)

                I am trying to restrain torsions and bond angles to do
        minimizations using sander_classic (do not want Cartesian coordinate
        restraints). I have tried to use the restrainTorsion command in xleap,
        which for all I can tell is working fine (desc [unit] tells me that the
        restraints I specified has been applied.) But, after I run sander and
        look at my coordinates I don't see the effect of the restraints.

It is possible that you are the first person to use actually
restrainTorsion and have discovered a bug in the way leap
writes the prmtop. This is because leap came into use around
the time that nmr restraints were implemented, and everyone
started using these. I think it would be reasonable to remove
the restrain* commands from leap at this point.

Hopefully your questions about the nmr restraints can be answered
and this will solve your problem.

Bill Ross
Received on Wed Jul 11 2001 - 15:40:55 PDT
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