AMBER Archive (2002)

Subject: do I need to mutate H1 atoms to HC in a "not really" perturbed part of a molecule ?

From: hagop demirdjian (hagop.demirdjian_at_ens.fr)
Date: Tue Oct 08 2002 - 09:51:50 CDT

Hi AMBER list,

a quick question about atom types and mutation,

I am mutating ethane to methanol.
In ethane, all H are HC type : 3(HC)CT-CT(HC)3
In methanol, the methyl hydrogens are H1 type : 3(H1)CT-OH-HO
Do I need to consider these hydrogen atoms perturbed too ? going from HC
to H1 type.
I am asking this question because angle value for HC-CT-OH is not
defined in parm99 (which is logical since that sequence does not exist !)

sorry if this is an obvious one,
Thank you,
Hagop.