AMBER Archive (2009)

Subject: [AMBER] SQM and AMBER

From: Jio M (jiomm_at_yahoo.com)
Date: Sat Dec 19 2009 - 00:36:05 CST

Dear AMBER users;

I didnt realy started my work on this topic but I have some queries.

I have a large organic molecule and hence can use GAFF for that (atoms
are less, antechamber can handle). I dont have problem in using hard
parameters like angle, bond length of GAFF. But for dihedral torsional
force constant and angle I want to derive from IR data and Scaled
Quantum Mechanics (SQM) data

But the problem is :

1) I would be using some higher level theory like B3LYP for SQM and
would get some charges on the atoms. For doing simulations, AMBER will
use its own charges like bcc or resp that will be different from B3LYP
derived in SQM. Can I use the dihedral force constants and dihedral
angles from SQM, additionally in frcmod file along with GAFF (GAFF for
hard parametrs).

My question relate to fact that I derived dihedral force constant
and  angle with charges that will be different from AMBER provided
charges for doing simulations, and using force const. and angle values
in frcmod file. Is this OK to do like this or else I should use same
charges as derived from SQM.

2) I think I cannot use resp charges, as suggested we should use HF/6-31G* for esp. But I am using B3LYP method.

Please suggest regarding this problem;

Thanks and regards;

JIomm

      
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