Thank you very much for your response. I am at the moment interested in doing
conformational search.
Using freeze groups in combination with conformational search does not
seem optimal...
Is there any good paper that explain nicely about doing the charge distribution
calculation?
You need to do an ab initio calculation on the system you want to
parametrize. This will give you the true charge distribution to which
you can fit a set of partial charges located on the nuclei. There are
several possibilities to do the fitting, check what the QM programs you
can use support. But in the end the charges are not too strongly
dependent on the fitting/level of QM. In addition you can sample several
configurations and use some sort of averaging to get the partial charge
(see RESP).
Gerrit
With regards,
Abu
----------------------------------------
Date: Tue, 11 Mar 2008 10:16:51 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Avoiding parameterization step
Hi All User,
I have been wondering whether it is advisable to avoid parametrization step by
freezing the atoms in MD
simulation.
Depends on what you want to do.
You most likely would still need the charge distribution, which is the
most difficult part of the parametrization part usually.
Bonded interactions can often be guessed by comparing to known residues.
Gerrit
With regards,
Abu
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