AMBER Archive (2003)

Subject: Re: AMBER: minimization error

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 14 2003 - 13:41:43 CDT

On Thu, Aug 14, 2003, Venkata S Koppuravuri wrote:
>
> I am trying to minimize a protien structure on one of our clusters. the
> simulation went fine, but when i checked the min.out file i got weird
> values for some of the parameters. below is a part of min.out file
>
> ----------------------------------
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -nan -nan 2.9855E+15 HB 224
>
> BOND = 16393.1733 ANGLE = 623.3094 DIHED = 463.8889
> VDWAALS = -nan EEL = -nan HBOND = 0.0000
> 1-4 VDW = 497.7016 1-4 EEL = 3080.5624 RESTRAINT = 0.0000
>

"nan" means "not a number". You almost certainly have two atoms on top
of each other in your initial structure. You need to fix this before
the minimization (or anything else) can proceed.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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