Just curious, did you have water in the system?
It helps us if you can be a bit more specific. "a protein structure" is
not considered too specific. As a consequence, you should expect
"something was wrong" in return which is not that specific either.
yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, August 14, 2003 2:42 PM
To: amber.scripps.edu
Subject: Re: AMBER: minimization error
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
>
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Received on Thu Aug 14 2003 - 22:53:00 PDT
