AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa calculation for calcium

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Tue Jun 13 2006 - 12:26:56 CDT

Thanks for your kind mail, but my question was different, I haven't
administrative privilege to edit the module file on linux cluster.

Navnit

Scott Pendley wrote:

> 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
> <mailto: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>
> > <mailto: 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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