On Thu, Oct 10, 2002, sxzheng wrote:
>
> I have a organic molecule to be perturbed.
> I have completed the process:saveamberparm. When I use
> "saveamberparmpert",there is many proper torsion parameters missed.I feel
> something confused as followed:
>
> ***Proper torsion parameers missing ***
> atom names:C12-C11-C10-C13
> atom types: c3-c3-c3-c2 =pert=> c3-c3-c3-c3
> Please add a dummy parameter of multiplicity 1
> for the no-pert types to your parameter set.
> -e.g. c3-c3-c3-c2 1 0.0 0. 1.
>
> At the same time ,it also advises to add a dummy parameter of multiplicity 2
> as:
> atom names:C12-C11-C10-C13
> atom types: c3-c3-c3-c2 =pert=> c3-c3-c3-c3
> Please add a dummy parameter of multiplicity 2
> for the no-pert types to your parameter set.
> -e.g. c3-c3-c3-c2 1 0.0 0. 2.
>
> While I think the PN parameter of torsion x -c3-c3-x should be 3.
> So why it advise 1 and 2 for PN that is conflictory and why it is not 3.
> further,why it's dummy parameter and what's the effection of the system.
>
You should read the original force field papers (say Cornell et al., and the
Weiner et al 1984 paper) for a discussion of rationales for having more
than just 3-fold torsions for things like x-c3-c3-x.
The amber program requires the same sets of torsions for non-perturbed and
perturbed. LEaP is just asking you to add a "dummy" (i.e. one with zero
force constant, and hence no effect) to satisfy that requirement. LEaP
does not just "do this automatically", since such a mismatch is often a sign
of some error, and thus wants to be sure this is what you really want to do.
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Oct 10 2002 - 11:37:40 PDT
