AMBER Archive (2008)

Subject: Re: AMBER: regarding segfault during energy minimization

From: Anamika Awasthi (aawasthi28_at_gmail.com)
Date: Thu May 01 2008 - 00:57:35 CDT

Dear Ross,
      Oxygen atom 50311 is of water, I am using Pymol for visualization and
I am not getting how can I fix this problem.
      My initial structure of protein seems okey. My protein is so big that
its tough to rorate or translate in pymol.
      Please help me and tell how can I do that?

       with regards
          Anamika

On Wed, Apr 30, 2008 at 11:10 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Anamika,
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 7.3878E+08 5.4632E+07 2.1205E+10 O 50311
>
> BOND = 635.4719 ANGLE = 3767.4121 DIHED =
> 18625.3499
> VDWAALS = ************* EEL = -509956.6162 HBOND =
> 0.0000
>
> 1-4 VDW = 8179.5683 1-4 EEL = 79691.9336 RESTRAINT =
> 0.0000
>
>
>
>
>
> You have two atoms sitting on top of each other. Note the *'s for VDWaals
> energy. This means the value is too big to fit in the space available in the
> output file. Also note GMAX of 10^10 Kcal/mol/A2 on a single atom!. You
> should take a careful look at your initial structure, particularly in the
> region of the Oxygen atom 50311. You will need to fix this clash before you
> can run the minimization.
>
>
>
> Ross
>
>
>
>
>
> /\
>
> \/
>
> |\oss Walker
>
>
>
> | Assistant Research Professor |
>
> | San Diego Supercomputer Center |
>
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
>
>
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>
>
>
>
>

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