AMBER Archive (2006)

Subject: Re: AMBER: Strange minimization output problem

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Sun Feb 05 2006 - 09:23:03 CST

Hi,
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 0.0000E+00 N 1
>
> BOND = 33.1578 ANGLE = 138.5896 DIHED = 540.6158
> VDWAALS = 4508907.4378 EEL = -3854.6022 EGB = NaN
> 1-4 VDW = 244.7324 1-4 EEL = 1984.2068 RESTRAINT = 0.0000
E(VDW) is huge and EGB isn't even a real number. So at least two atoms
seem to be much too close. There doesn't seem to be a bond between them
(otherwise E(BOND) would also be quite huge). Besides, one of them seems
to be neutral (otherwise I'd expect EEL to be enormous, too).

I'd
1) have a look at the structure (using VMD or a similar program).
2) try and minimize the structure with "diel=r", i.e. without GB and see
what happens.

God luck
Andreas 

-- 

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                        svrci_at_tbi.univie.ac.at
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