AMBER Archive (2009)

Subject: [AMBER] SQM and AMBER :again

From: Jio M (jiomm_at_yahoo.com)
Date: Wed Dec 23 2009 - 23:18:37 CST

Dear AMBER users;

I think I did not present my question "well" previously (with same subject).. Somebody please reply

I have query regarding AMBER and GAUSSIAN for Scaled Quantum

useage.

I have a organic molecule and hence can use GAFF (in Amber)(atoms

are less, antechamber of AMBER can handle). I dont have problem in
using hard parameters like angle, bond length of GAFF. But for dihedral
torsional

force constant and dihedral angle I want to derive from IR data and Scaled

Quantum Mechanics (SQM) data from GAUSSIAN and want to use it along with GAFF in AMBER

But the problem is :

I would be using some higher level theory like B3LYP for SQM and

would get some charges on the atoms in GAUSSIAN. For doing simulations, AMBER will

use its own charges like bcc or resp that will be different from B3LYP

derived in SQM.

I mean to say

1) can I use the force const and dihedral angle values from SQM  
for any charge method on atoms (like resp in amber) "or" else the
charges that were used to derive force const and dihedral value should
be used only for simulations in AMBER.

2) can I use the force constant and dihedral angle values for same
molecule optimised with HF/6-31G (because resp would require it do so)
"or" else the basis set that were used  derive force constant and
dihedral value should be used.

thanks and regards; HaPpY hOlIdAyS

JIomm

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber