RE: [AMBER-Developers] SCEE and SCNB removed

From: Ross Walker <>
Date: Wed, 10 Feb 2010 03:43:28 -0800

Hi Wei,

> Just want remind you that that sleap already handles 14 factor.
> currently it reads these factors from an extra section in the
> frcmod file, and write the 14 factor section to topology file. See the
> test case under test/sleap/14scale for example. But it
> should be fairly easy to modify the code so it should the format as you
> proposed.

This is good. We should probably have this turned on by default in gleap and
sleap. Can it be modified to use the following format and this is what I
will update the documentation to reflect.


CM-N2-CA-NC 1.1 180. 2. 1.2 2.0 dac
guess, 9/94
CB-N2-CA-NC 1.1 180. 2. 1.2 2.0 dac,
N2-NA-CA-NC 1.1 180. 2. 1.2 2.0 dac,


C -N -CT-C 1 0.00 0.0 -4. 1.2 2.0 four
amplitudes and
C -N -CT-C 1 0.42 0.0 -3. 1.2 2.0 phases
for phi
C -N -CT-C 1 0.27 0.0 -2. 1.2 2.0
C -N -CT-C 1 0.00 0.0 1. 1.2 2.0

Impropers should NOT have an SCEE/SCNB entry and should probably be set to
0.0 or -1.0 or similar when written to the prmtop file. I forget what we
currently have it do. In the event of multiple dihedral terms we should take
the first specification for the scee and scnb values and ignore all later

Note the code needs to be able to read the existing formats without the 1.2
and 2.0 and write default values to the prmtop value for these dihedrals.
This should default to 1.2 and 2.0 although we might want to have a
controlling set of env variables in gleap/sleap that allows the default
value to be adjusted, to say 1.0 if desired. Maybe SCEE_DEF and SCNB_DEF.

I plan to ONLY update the glycam and weiner et al parm files so everything
else will be left at the defaults.

Do you think it would be easy to make these same changes to xleap/tleap?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Wed Feb 10 2010 - 04:00:02 PST
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