AMBER Archive (2003)

Subject: Re: desolvation energy in mm_pbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Feb 04 2003 - 14:59:21 CST

Hi,

> Now I have another error message:
> Can't use an undefined value as an ARRAY reference at
> mm_pbsa_statistics.pm line 1234.

Did you check your XXX_com.all.out file if all values make sense there
(i.e. non is "nan" or something like this)? Otherwise you might need to
send me your files so that I can check what happens.

Best regards

Holger

>
> >From amber mail archive, there is one related problem
> but that problem is about metal ion. However I do not
> have any metals in my system. Here is my .in file:
>
> @GENERAL
> PREFIX 5TS_stability
> PATH ./snapshots/
> COMPLEX 1
> RECEPTOR 0
> LIGAND 0
> #
> COMPT 5bound.top
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> #
> @GB
> IGB 4
> SALTCON 0.00
> EXTDIEL 80.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> --- Michael Ford <mford_at_ccrc.uga.edu> wrote:
> > you CAN use just pb or gb. (in my experience, for
> > large molecules pb
> > isn't that useful)
> >
> > You need to be careful with which GB options you
> > choose (i.e. read the
> > references!)
> >
> >
> >
> > eric hu wrote:
> >
> > > Hi, in the mm_pbsa tutorial example 2, both pb and
> > gb
> > > are used for desolvation calculation. Why cannot
> > just
> > > use one of them? Also I do not have delphi. But I
> > have
> > > UHBD and wonder if anyone has some experience with
> > it.
> > > Thanks.
> > >
> > > Eric
> > >
> > > __________________________________________________
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> >
>
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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++