From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Dec 19 2003 - 16:25:19 CST
blushing.....
yes I figure that out a an hour ago and was too embarassed to post it to
the list....
Brian
On Fri, 19 Dec 2003, Jim Phillips wrote:
>
> Are there any angles or dihedrals for water in your psf file? It looks
> like you used "auto none" for your protein segments as well as water.
>
> -Jim
>
>
> On Fri, 19 Dec 2003, Brian Bennion wrote:
>
> > Hello
> >
> > I have a protein,ligand,water system that I am minimizing a compartment at
> > a time. Ie hold water constant while I minimize protein using the
> > fixedatoms switch and associated pdb files.
> >
> > During the minimization of protein only, my log doesn't register any
> > values for angles and Torsions, see log snippet below. (lines add for
> > clarity)
> >
> > Has anyone seen this behavior? I know I must have set something up
> > wrong....
> >
> > TIMING: 1000 CPU: 459.26, 0.4558/step Wall: 479.792, 0.468245/step, 0
> > hours remaining, 23163 kB of memory in use.
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP ELECT | VDW | |
> > BOUNDARY MISC | KINETIC | TOTAL TEMP
> > TOTAL2 TOTAL3 | TEMPAV | |
> > G PRESSURE |GPRESSURE | VOLUME |PRESSAVG
> > GPRESSAVG | | |
> > \/ \/ \/
> > ENERGY: 1000 148.8830 0.0000 0.0000
> > 103.9911 -570385.5058 -1214.2442
> > 0.0000 0.0000 0.0000 -571346.8759 0.0000
> > -571346.8759 -571346.8759 0.000
> > 0 -431.4039 -395.9418 332998.5650 -431.4039
> > -395.9418
> >
> > WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 1000
> > WRITING COORDINATES TO OUTPUT FILE AT STEP 1000
> > WRITING VELOCITIES TO OUTPUT FILE AT STEP 1000
> >
> >
> > --
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
> >
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 424-6605 ** *****************************************************************
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