AMBER Archive (2003)

Subject: RE: AMBER: minimization error

From: Yong Duan (yduan_at_udel.edu)
Date: Thu Aug 14 2003 - 15:56:54 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Thursday, August 14, 2003 2:42 PM
To: amber_at_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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