AMBER Archive (2009)

Subject: Re: [AMBER] normal modes calculation

From: chaitanya koppisetty (ashok_at_chalmers.se)
Date: Thu May 14 2009 - 03:51:28 CDT

Your structure should be in a minimal state (Grad atleast 10E-6) for a
reliable nmode calcualtion. Try minimizing your structure to that gradient
first before starting the nmode.

> Hi List,
>
> I get the following message when i use dielectric =1 or 2.0
>
> ***************** ***************** *****************
> step = 0
> F = 0.183600E+02 GRDMAX = 0.905302E+01 GNORM = 0.948202E+00
> E-NONB E-ELE E-HBOND E-BOND
> -0.52575E+03 -0.41202E+03 0.00000E+00
> 0.19635E+02
> E-ANGLE E-DIHED E-NB14 E-EEL14
> 0.59426E+02 0.52246E+03 0.20295E+03
> 0.15166E+03
> E-POL E-3BOD
> 0.00000E+00 0.00000E+00
> Root-mean-square gradient of input coords is 0.948202203680231
> This is greater than the requested maximum: 1.000000000000000E-003
>
> If I use dielectric=4 then the calculations terminate normally. I m using
> scee=1.2. I tried changing the number of cycles but no luck!
>
> Many thanks,
> Neha
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