AMBER Archive (2004)

Subject: Re: AMBER: minimization of GLH

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 05 2004 - 10:26:27 CDT

On Mon, Apr 05, 2004, Hailong Lin wrote:

> i am doing minimization of haloperoxidase in amber7. Glutamic acids were
> protonated by changing the residues name from GLU to GLH. The minimization
> failed due to linmin failure on the OE1 in one GLH at all time even though i
> have relaxed all the GLHs manually in LEap.
>
> .... RESTARTED DUE TO LINMIN FAILURE ...

> ntb=1, ntc=2,

This probably has nothing to do with GLU vs GLH, but to the fact that the
Amber minimization scheme doesn't know anything about SHAKE. The results
you obtain are to be expected.

If you are just minimizing prior to carrying out molecular dynamics
simulations, you are probably fine already. If you need to get a better
minimum, you must turn off shake.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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