Message: 10
Date: Sun, 29 Jan 2012 19:09:04 +0100
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] loading of fullerene2160
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20120129190904.eey4p79ksgs0k888.webmail.u-picardie.fr>
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Dear Gargi Borgohai,
> I have the pdb file of fullerene2160. I am trying to
> load the molecule, save the parameters and to give a homogenous charge
> distrbution on all the carbon atoms. Will you please let me know how can i
> do it successfully.
If you consider all the carbon atoms of your fullerene chemically
equivalent (as they should be - to be checked) and if the total charge
of your molecule is zero, this likely means the charge value of each
carbon equals zero.
I would check what charge values are used in the literature for your
molecule or similar ones...
regards, Francois
Respected Sir,
Thank you for your reply. I am using AMBER10. The
problem is that I am not even able to load the molecule in xLeap. The pdb
file of fullerene C60 can be loaded, but without
bond connectivity . Loading of frcmod and prepin files solve this problem.
But the problem arises with giant fullerenes like C720 and C2160. I think
the problem is related to frcmod and prepin files which I am not able to
generate for these molecules. To the best of my knowledge, antechamber can
not be used for molecules with large number of atoms. So please let me
know how to load the pdb files of these molecules and save the prmtop files.
Thanking
You.
Sincerely
Gargi Borgohain
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Received on Sun Jan 29 2012 - 21:00:02 PST
