AMBER Archive (2006)

Subject: AMBER: mm_pbsa calculation for calcium

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Mon Jun 12 2006 - 00:59:06 CDT

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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