AMBER Archive (2003)

Subject: Re: desolvation energy in mm_pbsa

From: eric hu (erichu_linux_at_yahoo.com)
Date: Tue Feb 04 2003 - 14:38:18 CST

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

>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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