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.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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Received on Wed May 20 2009 - 14:33:17 PDT
