AMBER Archive (2000)

Subject: Question?

From: Khatcharin Siriwong (siriwong_at_theochem.tu-muenchen.de)
Date: Thu Nov 23 2000 - 11:27:08 CST

Dear Sir,

I have some questions about setting amber parameters. I read in Amber 6
manual and practiced in amber tutorial, but I don't understand. Could
you please tell me that;
1. What condition do you use generalized Born model (GB)? with or
without solvent?
2. In Amber 6 manual, if IGB=3, it mean a calculation in vacuum (no
solvent) with a distance-dependent dielectric. Is the GB and PME
(particle-mesh Ewald) used in the case of IGB=3?
3. How do you set the parameters if you want to run MD simulation with
both the GB and PME?

I am looking forward your answers and thank you very much for your
kindness.

Sincerely Yours,
Khatcharin Siriwong