AMBER Archive (2005)

Subject: AMBER: Making prep file of sugar derivative

From: Toshifumi Yui (tyui_at_cc.miyazaki-u.ac.jp)
Date: Thu Sep 29 2005 - 07:02:12 CDT

Dear Amber Folks

My molecular system involves a protonated glucuronic acid.

The glycam 04 parameter set comprises the prep file for glucuronic acid and
related parameters but it is an ionic state (-COO). Therefore, I have
encoutered the "missing parameters" message as regarding -COOH group,
although after making the prep file for a protonated glucuronic acid.

My solution for this trouble is to complement the glycam parameters with
those of the protonated glutamic and aspartic acids in parm 99, by changing
the atom type name, let's say, from CT to CG. This, however, is not working
at present.

Would please tell me a list for possible parameter entories
for -C(aliphatic)-COOH group in the parm99.dat file (e.g. CT-CT-O-OH, and
so on), if my idea for the trouble is OK.

Thank you.

Toshifumi Yui
Miyazaki University
Miyazaki, 889-2192 Japan

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