Dear Todd,
I am sure more people will tel you this, but please, please please do
not use Amber 94 parameters !
They are not recomended anymore, and we have better stuff out there.
Try instead ff99SB or ff03.
Adrian
todd.semichem.com wrote:
> Hello,
>
> I am writing some code to assign AMBER 94 charges to proteins.
>
> I am using the data in the amino94.in, aminoct94.in and aminont94. files
> from the amber10.ffparms download.
>
> These files contain 3 sets of charge data for LYS: non-terminal residue
> form, amino-terminal (NH3+ end group) residue form and carboxyl-terminal
> (COO- end group) residue form).
>
> However, only data for the non-terminal residue form of LYN (the
> deprotonated form of Lysine, where the R group is neutral) appears to be
> present.
>
> Aplogies if this data exists and I'm not finding it. But if not, what is
> the recommended procedure to deal with charges for terminal LYN residues?
>
> Similarly, data for the terminal forms of GLH, ASH and CYM appears to be
> absent.
>
> Lastly, does charge data exist for the neutral end group forms of the
> amino-terminal and carboxy-terminal residues?
>
> Thanks!
>
> Todd
>
>
>
>
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>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Wed May 20 2009 - 15:21:43 PDT
