From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Sep 02 2008 - 22:39:34 CDT
Are you sure they should be there? Sometimes a long bond comes about
during system preparation by design, but if you didn't mean to have it
there (for example, by moving a fragment of the protein away from the
rest of it) this is due to some problem in your initial coordinates.
If the long bonds should indeed be there, you should be able to get by
this problem by including a margin statement (eg, margin 20). You'll
certainly need to minimize for more than 20 steps to avoid having the
system explode immediately after minimization.
Lam T Nguyen wrote:
> Thanks Peter,
> Yes, there are indeed long bonds.
> Peter Freddolino wrote:
>> Hi Lam,
>> usually this indicates that there's a bond that is unrealistically
>> long; the very high BOND energy you have here also points in that
>> direction. Have you loaded your structure into vmd with both the psf
>> and pdb? Are there any long bonds present?
>> Lam T Nguyen wrote:
>>> Hi all,
>>> I recently got these warning when I increased the number of atom ~
>>> 80000. That included increasing in number of residue, group ...
>>> At first I thought there would be some problem with the system
>>> setup. I tested with smaller number of atom (like ~50000 atoms) and
>>> it's OK. I've been looking at suggestion for possible errors, like
>>> ones in the structure, etc, but it did not help much.
>>> Here are the warnings:
>>> TCL: Minimizing for 20 steps
>>> Warning: Bad global exclusion count, possible error!
>>> Warning: Increasing cutoff during minimization may avoid this.
>>> Warning: Bad global bond count!
>>> ETITLE: TS BOND ANGLE
>>> DIHED IMPRP ELECT VDW
>>> BOUNDARY MISC KINETIC TOTAL
>>> TEMP TOTAL2 TOTAL3 TEMPAVG
>>> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>> ENERGY: 0 7675440.0997 15.0940 0.0000
>>> 0.0000 140.7825 99999999.9999 0.0000
>>> 0.0000 0.0000 99999999.9999 0.0000
>>> 99999999.9999 99999999.9999 0.0000
>>> 639.3370 639.3370 99999999.9999 639.3370 639.3370
>>> any help please.
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