On Fri, Apr 29, 2011, Wei Zhang wrote:
>
> About the sleap issue of two improper dihedrals, what do you think
> would be the correct approach here?
> If we are going to choose from one of the two, what is the criteria for
> choosing?
The criterion is this: the central atom is always at position 3; positions 1,2
and 4 are filled in alphabetical order by atom type.
> > Consider these atom types relevant to an improper dihedral: CG, N, H, C
> >
> > And these two impropers:
> > parm99 X -X -N -H 1.0 180. 2. JCC,7,(1986),230
> > Glycam06 X -X -N -CG 1.5 180. 2. X -X -N -H
First, I don't understand the X-X-N-H comment at the end of the glycam06
line: what is it supposed to mean, especially since the force constant
here is *not* the same as in parm99? Second, (assuming that N is the
central atom), the correct order should be C-CG-N-H. Third, as I
understand it(?) CG is a glycam-specific atom type. We appear to have a
problem if both X-X-N-H and X-X-N-CG wild cards match, and have different
force constants.
It looks like (a) the glycam06 file is subtly inconsistent with parm99; (b)
that wild cards are again causing trouble, especially since the chemical
environment of atom type "N" in glycam is very different than atom type "N" in
proteins.
One way forward is to replace the wild cards above with specific impropers;
that has been urged for some time, and is probably needed more than ever.
....dac
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Received on Sun May 01 2011 - 09:30:03 PDT
