Dear Hari,
Some of your groupments/peptide look distorded... Is it normal ?
Are you sure hf/3-21g* is a suitable theory level for this type of complex.
I suggest you to use the R.E.D.-III.3. tools available .
http://q4md-forcefieldtools.org/RED/
regards, Francois
> I have problems finding amber parameters and resp charge for iron (or zinc,
> which can be used to replace iron) in the molecule containing an iron atom
> and its ligands (octahedral structure) containing five amino acids. The
> structure was taken from the crystal structure 1AIJ and the amino acids were
> neutralized by adding extra amino or carboxyl groups. I used amber10 package
> to calculate the parameters. The program did not recognize zinc atom type
> and considered as a dummy atom (DU) with zero charge and no force and Van
> der Waal parameters.
>
> Would you please help me to fix this problem? I have also attached Gaussian
> output file here.
>
> Sincerely,
>
> Hari P. Lamichhane
> Graduate student in Physics,
> GSU, Atlanta
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Received on Thu Jan 07 2010 - 14:00:02 PST
