AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa calculation for calcium

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Mon Jun 12 2006 - 16:42:59 CDT

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> 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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