From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Dec 19 2003 - 16:23:36 CST
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 **
> *****************************************************************
>
>
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