AMBER Archive (2006)

Subject: Re: AMBER: Strange minimization output problem

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Sat Feb 04 2006 - 10:12:19 CST

Hi Andy,
             Please check your prmcrd file. Normally, NaN error caused
by poor starting structure otherwise check the cutoff value of the
minimization.

..anand

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ANANDA RAMA KRISHNAN .S
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Martin Luther university
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e-mail: ananda.selvaraj_at_chemie.uni-halle.de
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----- Original Message -----
From: andy ng <andy810915_at_gmail.com>
Date: Saturday, February 4, 2006 1:39 pm
Subject: AMBER: Strange minimization output problem

> Dear User,
>
> Does anyone know what cause this strange problem in the complex output
> file of my minimization?
>
> I am following the tutorial2 @
>
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_two/index.htm
> except I have my own WW domain and peptide.
> I was able to run the minimization and dynamic on peptide and protein
> but not the complex.
>
> below is the output file
> --------------------------------------------------------------------
> ------------
> 4. RESULTS
> --------------------------------------------------------------------
> ------------
>
>
>
> 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
>
>
>
> It just stop there and no more result is coming out.
> The prmtop and inpcrd did not complain anything when i created them
> in xleap.
> Any idea what could be the problem?
>
> Andy
> --------------------------------------------------------------------
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