AMBER Archive (2006)

Subject: AMBER: question about solvatecap commander

From: aini_at_umdnj.edu
Date: Tue Mar 07 2006 - 20:46:41 CST

Dear Amber users,

  I am trying to perform a MD simulation on the extracellular loop region of
a transmembrane protein. I used solvatecap to add water around this region.
Then I want to minimize the protein first. And sander is just hanging and
didn't proceed.
I checked the .out file. See below
| Flags:
   
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info not found in inpcrd
|Largest sphere to fit in unit cell has radius = NaN

The program seems to stop here. Does anyone know what might be the problem?
And what will be the best way if I just want to simulate the loop region
without altering the other part of the protein?
Thanks a lot! Any help would be appreciated.

aini 

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