> > 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:
Heh... yeah... good question. We're hunting the origin of it now. Obviously, it isn't parm94 or parm99.
> 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.
We do require a larger force constant to hold certain bits planar the sort of environment oligosacchardes are likely to create. 1.5 might not be enough. But, I think we can rearrange things so that there are not inconsistencies: that N gets treated how it needs to be treated in the different environments. We're working on that, too.
> 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.
Somehow, I suspect that protocol was not strictly respected in a variety of instances (parm file, code, etc.).
> 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.
We're discussing this, too.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: David A. Case [case.biomaps.rutgers.edu]
Sent: Sunday, May 01, 2011 12:15 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] alternates to sleap (plus new sleap bug)
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
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon May 02 2011 - 09:00:04 PDT
