In order to do a proper test of tleap versus sleap, we did the following:
1. Hacked 1-4 scaling writes into tleap.
2. Wrote a separate program, independently, that adds SCEE/SCNB to an existing top.
Then, we compared output from post-processing an existing trajectory for a system containing both a glycan and a protein using top files produced by:
1. old tleap plain -vs- new tleap with SCEE/SCNB written out, but manually changed back to AMBER defaults.
2. new tleap with SCEE/SCNB -vs- the post-processor we wrote
3. new tleap with SCEE/SCNB -vs- sleap with SCEE/SCNB
The results from 1 were identical, as were the results from 2. There was a small difference in the sleap dihedrals from 3 (explained below).
If you agree with our procedure and with our assessment of the sleap dihedral issue, we will push the changes to tleap.
We'll also make the post-processor available on our site, but we can add it to Amber, too, if you want. We'll probably post the tleap mods to our site, too, to make sure the carb folks see them.
Here's the sleap issue.
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
When tleap generates a top file, the CG-N-C-H improper dihedral is specified only once. When sleap generates the top file, the improper is defined twice (once as CG-N-C-H and once as CG-C-N-H). We also checked comparing old tleap (no SCEE/SCNB) and sleap without using "write14scale". The improper is again defined twice by sleap and once by tleap.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
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Received on Thu Apr 28 2011 - 15:00:02 PDT
