AMBER Archive (2002)

Subject: Re: mm_pbsa

From: Mahadevan Seetharaman (maha_at_vwl.medc.umn.edu)
Date: Sun Sep 22 2002 - 21:07:27 CDT

Hi,

I was having exactly the same problem. Does that mean Na+ and K+ ions have
not been parameterzed for mm_pbsa? Is there an alternative, other then
changing the code?

Thanx
Mahadevan

On Sun, 22 Sep 2002, Holger Gohlke wrote:

> Sue Heavner wrote:
> >
> > Hi:
> > I am using mm_pbsa in amber7. I would like to include Na ions in the
> > calculations but keep getting errors including "bad atom type: IP"
> > and
> > "Can't use an undefined value as an ARRAY reference at
> > /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.". I
> > think maybe I need to modify the code in mdread.f. Can anybody help?
> >
> > Thank-you, Sue Heavner
>
> Dear Sue,
>
> the "bad atom type" message indeed comes from the parameter assignment
> for SA calculations within mdread.f (and the "... undefined value ..."
> is a follow up then). You might have a look at the section for Mg ions
> there as a starting point to extend the code for your purposes.
>
> Best regards
>
> Holger
>
> --
> +++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
> Dept. of Molecular Biology, TPC15
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> La Jolla CA 92037 USA
> phone: +1-858-784-9788
> fax: +1-858-784-8896
> email: gohlke_at_scripps.edu
> +++++++++++++++++++++++++++++++++++++++++++++
>