AMBER Archive (2009)

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

From: todd_at_semichem.com
Date: Sat May 09 2009 - 11:27:52 CDT

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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