Re: dummy torsional parameters

From: David A. Case <>
Date: Thu 27 Jun 2002 08:38:49 -0700

On Thu, Jun 27, 2002, Giulio Rastelli wrote:

> Leap suggest the addition of several dummy torsional parameters
> for construction of a topology with perturbation. Some of them are
> meaningful to me (i.e. the parameters related to atoms that disappear
> at lambda=0; these correspond to dummy atoms with zero torsional
> constants that need to be defined). Others
> relate to atom types that change during FEP but that are not dummy
> atoms.
> Since these last parameters are already present in parm99, it is not
> clear
> to me why leap is complaining about them.

I can't comment without more information; if the parameters are actually
in parm99, LEaP should not complain about them being missing.

> Last question, adding general parameters (like X-CT-DH-X) does not solve
> the problem. Do they need to be specific parameters?

This should be OK. Check if the missing parameters are for improper torsions;
they need to go into a different section of the file than general parameters.
Also, I think (if you are directly modifying parm99.dat, rather than
constructing a frcmod file) that generic parameters need to be placed ahead
of specific torsional parameters.

..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 27 2002 - 08:38:49 PDT
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