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 - 02:45:32 CDT

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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