You could try to make a local version of mm_pbsa but I must warm you that
this is more trouble than it is worth. If I were you, I would contact the
system administrator and make a detail request of them to make the changes.
If you wish to make the local versions let me know at my email address (not
the reflector) and I can walk you through it, though I highly recommend
going through your sys admin.
Scott
On 6/13/06, Navnit Kumar Mishra <navnit.chemi.muni.cz> wrote:
>
> 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.chemi.muni.cz
> > <mailto:navnit.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.chemi.muni.cz
> > <mailto:navnit.chemi.muni.cz>
> > > <mailto: navnit.chemi.muni.cz <mailto:navnit.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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Received on Wed Jun 14 2006 - 06:07:18 PDT
