AMBER Archive (2008)

Subject: Re: AMBER: Iron-Sulfur Cluster

From: Justine Condo (j-shaw_at_northwestern.edu)
Date: Fri May 30 2008 - 12:52:24 CDT

I use a program called HARLEM to set up my MD simulations (top file etc)
for AMBER that have metal complexes in them. Try taking a look:
http://www.kurnikov.org/harlem_main.html

Good Luck!
Justine

On Fri, May 30, 2008 at 4:46 AM, Joachim Reichelt <
Joachim.Reichelt_at_helmholtz-hzi.de> wrote:

> Hi,
>
> does anyone know how to get Fe4S4 Clusters into amber?
> antechamber does not like it:
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
>
> as mopac does not know anything about Fe
> --
> Joachim
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-- 
-*****************************
Justine Shaw-Condo -Ph.D. Candidate
Ratner and Meade Groups
Northwestern U.
Office: 4039 Nano
Phone: 847 467 4991
Web: http://www.justinechem.com
Email: j-shaw_at_northwestern.edu
*************************************

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