Re: amber-developers: improper dihedrals

From: David A. Case <>
Date: Tue, 24 Feb 2004 15:32:03 -0700

On Tue, Feb 24, 2004, Guanglei Cui wrote:
> I'm using antechamber in amber8 to create prepin file for isoprene-like
> molecules. antechamber added two improper torsions in the generated
> prepin file, but it seems leap likes to use different set of atoms for
> the definition. In leap.log, the message isn't quite clear to me if the
> improper torsions are applied.
> ---
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for c3-ha-c2-c2
> atoms are: C2 H6 C3 C4
> ** Warning: No sp2 improper torsion term for c2-c3-c2-c3
> atoms are: C3 C6 C4 C5

The above means the following: the program thinks you have a carbon bonded
to three other atoms (an "sp2" carbon, in its lingo), and that therefore,
you might want an improper torsion about that atom. However, it could not
find any parameters for such a torsion, and hence, did not put anything
This could be a limitation of the antechamber/parmchk programs.

> old PREP-specified impropers:
> <MOL 1>: C4 C2 C3 H6
> <MOL 1>: C3 C6 C4 C5
> total 0 improper torsions applied
> 2 improper torsions in old prep form

Above info is for information purposes only; LEaP ignores the PREP
(except to print them out as above).

> Does this look like the improper torsion has been taken care of? Thanks.

No; depending on your actual structure, you may be missing some impropers
that you ought to have. (Junmei, of course, can give the *real* answers


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Apr 05 2006 - 23:50:05 PDT
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