AMBER Archive (2005)

Subject: RE: AMBER: problem with gb md

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 05 2005 - 23:47:40 CDT

Dear Emilia,

> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 1 nan nan 0.0000E+00
> C34 1
>
> BOND = 199.1390 ANGLE = 606.5759 DIHED
> = 2318.4901
> VDWAALS = 134604.7930 EEL = -18304.6508 EGB
> = nan
> 1-4 VDW = 1344.4585 1-4 EEL = 11078.6900 RESTRAINT
> = 0.0000
> ==============================================================
> ============

Your VDWAALS term is pretty huge which suggests that there is something very
wrong with your initial structure. I suggest you check it carefully, you
likely have two atoms sitting on top of each other.

Try using the check command in xleap and see if any atoms are closer than an
angstrom or so.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross_at_rosswalker.co.uk |
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