AMBER Archive (2004)

Subject: Re: AMBER: minimization of GLH

From: Hailong Lin (hailong.lin_at_stud.man.ac.uk)
Date: Mon Apr 05 2004 - 10:51:47 CDT

yes, that is the minimization before a MD. i do need a better minimization.
With this minimized structure,the equilibration and the MD can not be
finished due to the large force in the system:
' vlimit exceed' and
' EWALD BOMB in subroutine ewald_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander'
if i turn off shake, the minimization stopped with huge RMS '7.6944E+10' and
'1-4 EEL = *********'

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Monday, April 05, 2004 4:26 PM
Subject: Re: AMBER: minimization of GLH

> 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
> ==================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu