AMBER Archive (2008)

Subject: Re: AMBER: Zn2+ Bondi radius value

From: Enguerran Vanquelef (enguerran.vanquelef_at_q4md-forcefieldtools.org)
Date: Wed Oct 08 2008 - 06:55:21 CDT

Hi Sergey

If you have received my first mail, please ignore it.

maybe it can help you : I have found _Zn_ radius at 1.53 angstrom (see
http://www.answerbag.com/q_view/692420)

and after another better search, Zn2+ radius at 0.74 angstrom (see
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=eurekah.section.37633)

regards,

Enguerran Vanquelef

Quoting Sergey Samsonov <sergeys_at_biotec.tu-dresden.de>:

> Hi,
>
> I have a Zn2+ ion in MM-GBSA calculations. I get an error:
>
> No radius found for ZN 9240 in residue ZN 576
> Died at
> /group/bioinfp/soft/linux/amber8-32/src/mm_pbsa/mm_pbsa_calceneent.pm
> line 486, <PDB> line 9243.
>
> I know that in order to make it work I have to add the line to
> $AMBERHOME/src/mm_pbsa/mm_pbsa_calceneent.pm :
>
> "ZN" => Bondi radius value + 1.400,
>
> Do you know what is the value for Zn2+ ion? I tried to find it in the
> web but failed.
>
> Thank you very much in advance and best regards,
>
> Sergey
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