AMBER Archive (2005)

Subject: RE: AMBER: minimization stuck problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Aug 21 2005 - 15:02:09 CDT

Dear Pawel,

> I have maked cut bigger (15) and EEL is now very big. I hope it's
> not too big:

There is not really a concept of too big here, short of it hitting
-infinity. Your system is obviously quite large which is why the
electrostatic term is such a big negative number. Note it is possible to
gets *****'s printed in the output file. If you get this it does not
necessarily mean an error. It simply means that the value is too big to fit
in the space allocated in the output file. However, if you do see ***'s in
the output file you should always look at things carefully.

> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 40 -8.6709E+05 6.4349E+01 2.4613E+02 O
> 37174
>
> BOND = 205.7242 ANGLE = 820.3092 DIHED =
> 2463.7349
> VDWAALS = 15054.8365 EEL = -896452.7636 HBOND
> =
> 0.0000
> 1-4 VDW = 898.4925 1-4 EEL = 9923.3598 RESTRAINT
> =
> 0.0000
>
>
> Is there anything strange that you see in my output or input?

This looks fine to me. Although you don't say why you are not using PME.

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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