AMBER Archive (2009)

Subject: Re: [AMBER] normal mode analysis

From: Hannes Wallnoefer (Hannes.Wallnoefer_at_uibk.ac.at)
Date: Mon May 04 2009 - 10:56:11 CDT

Hi,

It seems as if you are right. I changed the default of the mm_pbsa.pl script for
ntxo from 0 to 1, because the default is not allowed in amber10 any more. If i
use amber9 with ntxo = 0 minimization the nmode tool works fine.
Is there an alternative to using amber9 for the normal mode analysis?

Best regards,
Hannes

Zitat von "David A. Case" <case_at_biomaps.rutgers.edu>:

> On Mon, May 04, 2009, Hannes Wallnoefer wrote:
> >
> > I use the mm_pbsa.pl script to evaluate the entropic contribution to a free
> > energy of binding of protein-ligand complexes in amber10. The snapshot
> > extraction and the minimization works fine, but when the script starts the
> > nmode tool the following error appears:
> > forrtl: severe (39): error during read, unit 53, file sanmin_com.1.restrt
>
> Check to see if the nmode calculation is expecting an unformatted input
> file, and if sanmin_com.1.restrt might be formatted. (Just a guess, but
> worth checking, since it would explain the error message.)
>
> ...dac
>
>
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