AMBER Archive (2009)

Subject: Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.

From: Adrian Roitberg (
Date: Sat May 09 2009 - 13:07:08 CDT

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 wrote:
> Hello,
> I am writing some code to assign AMBER 94 charges to proteins.
> I am using the data in the, 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
> _______________________________________________
> AMBER mailing list

                            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

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