On Mon, 2014-01-06 at 00:52 +0000, Allen, Scott Edward wrote:
> Hello,
>
> I'm trying to parametrize a dihedral in my small molecule. I find that when I incorporate my results into my .frcmod file, AMBER (tleap?) only reads the second term of the X -ca-cc-X dihedral (the phase=180 term). Has anyone had a similar problem? The full text of the .frcmod file is given below.
What makes you say this? Did you use ParmEd or rdparm to verify that
the first term is missing from the relevant torsion terms?
Also note that "X -ca-cc-X " is only used when a specific torsion is not
present in any of the parameter databases. It's possible that one of
the terms you hoped to modify with your torsion wild-card has a specific
definition in the gaff.dat file. In this case, the only way to override
that torsion term is to use specific torsions (i.e., with full atom
types as the first and last atoms rather than wildcards).
HTH,
Jason
>
> Thank you,
> Scott Allen
>
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
> X -ca-cc-X 4 1.800 0.000 -1.000 from GA
> X -ca-cc-X 4 3.500 180.000 2.000 from GA
> cc-ss-cc-cd 1 1.100 180.000 2.000 same as X -c2-ss-X
> cc-ss-cc-h4 1 1.100 180.000 2.000 same as X -c2-ss-X
> cc-ss-cc-nd 1 1.100 180.000 2.000 same as X -c2-ss-X
> cc-ss-cc-ca 1 1.100 180.000 2.000 same as X -c2-ss-X
>
> IMPROPER
> ca-nd-cc-ss 1.1 180.0 2.0 Using default value
> cc-h4-cd-nd 1.1 180.0 2.0 Using default value
> cd-h4-cc-ss 1.1 180.0 2.0 Using default value
> ca-cc-ca-nb 1.1 180.0 2.0 Using default value
> ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
> ca-h4-ca-nb 1.1 180.0 2.0 Using default value
>
> NONBON
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 06 2014 - 10:00:03 PST
