AMBER Archive (2003)

Subject: new amino acid residues

From: Nick Polfer (prrls03_at_holyrood.ed.ac.uk)
Date: Thu Jan 30 2003 - 06:58:41 CST

Dear Amber

I am trying to make some new amino acid residues which are only slightly
different to ones existing in AMBER. I have followed the antechamber
procedure, generated new charges using G98 and resp, have successfully got
a name.prepin and corresponding frcmod files.

One of the residues I tried to make is a 'protonated amidated C-terminal
glycine'. This residue was made as an incomplete molecule; i.e. the
nitrogen has an open valence.

Should I stick with the gaff suggested parameters or could I (my preferred
route) 'translate' these into parm99.dat format atom types?

Since I want to use these residues to make peptides (in Xleap) which I
then want to compare to other peptides completely generated from standard
AMBER residues, I would prefer if they could all be in the same format.

Can somebody please advise me on the flags I need to use to convert the
format either in antechamber or xleap?

cheers

Nick