AMBER Archive (2000)

Subject: Can I use heme prameters with param94 ?

From: Kazuki Shinoda (shinoda_at_biol2.bio.nagoya-u.ac.jp)
Date: Mon Feb 21 2000 - 05:42:29 CST


Dear AMBER users,

I have performed MD simulations with param94 and db94. Because my
system has been constituted by only a protein and solvent water, everything
has been O.K.. But now, I must treat a system which includes a heme-protein.
I want to continue using param94 and db94 because I want to use neutral-Asp
and neutral-Glu.

My question is whether can I use the all-atom heme parameter set (heme-all.
in and frcmod.hemall) that is on the AMBER home-page with param94 and
db94 ? If some modifications are required, do someone has any information
about them ?

Any information will be appreciated.

Best regards,
Kazuki

================================================
 Kazuki Shinoda, MC2
 Division of Biological Science, Graduate school of Science
 Nagoya University, Chikusa, Nagoya 464-8602, Japan

 E-mail : shinoda_at_biol2.bio.nagoya-u.ac.jp
 URL: http://bio.nagoya-u.ac.jp:8001/~kazuki/kazuki.html
================================================