Armin,
I have seen that error when mm_pbsa is try to process snapshots and
there are none available. As GC is marked zero, it assumes that you
are not creating individual snapshots from a given trajectories. Is
this what you wish to do?
SURFTEN and SURFOFF are specific to the type of GB or PB that you are
trying to perform. For a good referrence on this and mm_pbsa in
general see "Converging Free Energy Estimates: MM-PB(GB)SA Studies on
the Protein-Protein Complex Ras-Raf" Gohlke and Case. J Comput Chem
25:238-250 2004
On 7/11/05, opitz.che.udel.edu <opitz.che.udel.edu> wrote:
> I'm trying to run MM_PBSA in Amber 7. I get the following error message:
> Can't use an undefined value as an ARRAY reference at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.
>
> I don't know if this is due to something I input or if there is some
> other problem. My input is shown below.
>
> Furthermore, I was also wondering if SURFTEN and SURFOFF need to be
> changed and how I would go about deciding what value is "correct". Also,
> I just copied the atmtypenumbers from the mm_pbsa folder as is. Are these
> numbers general or case specific?
>
> Best Regards,
>
> Armin
>
> ################################################################################
> .GENERAL
> PREFIX test
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 0
> LIGAND 0
> #
> COMPT ./mans.prmtop
> RECPT
> LIGPT
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 0
> MS 1
> #
> NM 0
> #
> ################################################################################
> .GB
> #
> IGB 1
> SALTCON 0.00
> EXTDIEL 80.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> ################################################################################
> .MS
> #
> PROBE 1.4
> RADII ./atmtypenumbers
> #
> #################################################################################
>
>
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Received on Mon Jul 11 2005 - 19:53:00 PDT
