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.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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
--
-*****************************
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.northwestern.edu
*************************************
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 01 2008 - 06:08:01 PDT
