Re: amber-developers: improper dihedrals

From: Guanglei Cui <>
Date: Tue, 24 Feb 2004 16:34:41 -0700

Thanks. I looked at gaff.dat/improper dihedral section and found this
general term,

X -X -X -X 1.1 180. 2. dac, 10/94

why didn't leap use this for the found improper dihedrals? I played with
parmchk a bit. I deleted the two improper dihedrals from the antechamber
generated prepin. But it seems parmchk didn't restore them in the frcmod

David A. Case wrote:

> 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
> to three other atoms (an "sp2" carbon, in its lingo), and that
> you might want an improper torsion about that atom. However, it could
> 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
> that you ought to have. (Junmei, of course, can give the *real* answers
> ...dac
Received on Wed Apr 05 2006 - 23:50:05 PDT
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