>
>I am looking for parameters for polyunsaturated docosahexaenoyl chain.
>Could
>you help me , please?
In my opinion and recent experience you might want to try GAFF (general
amber force field), if the polyunsaturated docosahexaenoyl chain is not a
part of any modified biomolecule...You can therefore use ANTECHAMBER and
PARMCHK..etc.. like it is explained in antechamber tutorials..GAFF has
parameters for many non-biomolecular chemical entities...and my recent MD
simulations with GAFF have been very satisfactory....
....also you can get automatically calculated AM1-BCC charges which might
turn out to be of very good quality and its a time saving approach....
On the other hand if you are adamant on deriving your own parameters you
wiil have to run RESP calculation for charges, copy the bond and angle
parameters based on similarity and for torsions (WHICH ARE MOST IMPORTANT)
you have to run gaussian scans + SPASMS program....etc.
-Vineet
"The future belongs to those who believe in the beauty of their dreams"
-Eleanor Roosevelt
>From: "Ross Walker" <ross.rosswalker.co.uk>
>Reply-To: amber.scripps.edu
>To: <amber.scripps.edu>
>CC: <michalwitt.wp.pl>
>Subject: FW: AMBER: parametrization problem
>Date: Fri, 14 Jan 2005 14:39:12 -0800
>
>Dear Michal
>
>I have forwarded your message to the amber mailing list where people may be
>able to help.
>
> _____
>
>From: michal [mailto:michalwitt.wp.pl]
>Sent: 12 December 2004 08:23
>To: ross.rosswalker.co.uk
>Subject: RE: AMBER: parametrization problem
>
>
>Dear Sir/Madam,
>
>I am looking for parameters for polyunsaturated docosahexaenoyl chain.
>Could
>you help me , please?
>Magdalena Witt
>
>e-mail: mwitt.wp.pl
>
>University of Gdansk
>Faculty of Chemistry
>Departament of Molecular Moeling
>Poland
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Received on Sat Jan 15 2005 - 11:52:59 PST
