AMBER Archive (2004)

Subject: Re: AMBER: question about mm-pbsa

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon May 10 2004 - 20:10:09 CDT

Hi Aini,

Have you checked if your *all.out files contain a line for surface value
on the first snapshot? If no surface is available, mm_pbsa usually takes
the number from the snapshot before, but fails if that happens on the very
first snapshot.

I usually copied the surface line from the last snapshot into the first
one in the all.out files to solve this.

Regards,

Thomas

On Mon, 10 May 2004 aini_at_UMDNJ.EDU wrote:

> Dear Amber users,
>
> I am using MM_PBSA (amber 7) to calculate free energies of binding of a
> complex on a red hat linux machine. I followed the example mm_pbsa.in file
> in /amber7/src/examples/03_MMPBSA_Binding. I got *_com.all.out.save,
> *_lig.all.out.save and *_rec.all.out.save. However, when the progam went to
> statistics step, an error message
> "use of uninitialized value in multiplication (*) at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1323.
>
> Program stopped without *_statistics.out.save. Does someone know what may
> cause this?
> Thank you very much!
>
> aini
> -----------------------------------------------------------------------
> 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