AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa calculation for calcium

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue Jun 13 2006 - 11:20:42 CDT

This is one of those fun experiences in life when you learn things on the
job. You will want to hand edit (emacs or vi) and add you radii to the
list. Since this is written in perl, you don't have to recompile. I think
the directions should be pretty straight forward but if you have any
problems, email me directly.

Scott

On 6/13/06, Navnit Kumar Mishra <navnit_at_chemi.muni.cz> wrote:
>
> Thanks Scott,
>
> I got the parameter section for atom and it is in the file
> mm_pbsa_calceneent.pm, as I am just a common user of the linux cluster,
> I haven't opportunity to edit the file. Is there any option to export my
> atom type into the molsurf section.
>
> Thanking you,
> Navnit
>
>
> Scott Pendley wrote:
>
> > Navnit,
> >
> > This message is related to the molsurf program, not to delphi. You
> > will need to go through the mm_pbsa perl modules and add calcium
> > parameters into the molsurf input creation part.
> >
> > Scott
> >
> > On 6/11/06, *Navnit Kumar Mishra* <navnit_at_chemi.muni.cz
> > <mailto:navnit_at_chemi.muni.cz>> wrote:
> >
> >
> > Hello everybody;
> >
> > I am trying mmpbsa, I got problem with my system due to calcium
> > which I
> > defined as 'KA'. As it is mentioned in manual
> > and also in Example that I can define radius and charge for
> > all atom in
> > seprate file as my_amber94_delphi.crg and my_parse_delphi.siz, am
> > I right?
> >
> > I defined it as
> > KA CAL 9 2.0000 in delphi.crg
> > and
> > KA 1.79 in delphi.siz
> >
> > but when I excuted the mm_pbsa.pl, I got the message
> >
> > died as output, src/mm_pbsa/mm_pbsa_calceneent.pm line 485, <PDB>
> > line 3258
> > and in log file I got error
> > No radius found for KA
> >
> > As I know there is no parametrs for calcium, is it possible to do
> > it, if
> > yes how?
> >
> > Thanks for any suggestion,
> >
> > Navnit
> >
> >
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