AMBER Archive (2008)

Subject: Re: AMBER: AMBER parameters for Chlorophyll

From: David LeBard (david.lebard_at_asu.edu)
Date: Sat Feb 16 2008 - 11:25:51 CST

Hi Sreeja,

Marchi and coworkers have already developed all needed parameters for the
simulation of bacteriochlorophyll using the AMBER force field [1]. Although
due to some strange table limitations in the Journal of Computational
Chemistry (Wiley, really), I believe the supplemental data are no longer
available online so you may need to talk to Prof. Marchi directly in order
to obtain them. Also I don't know how much it will help, but force field
parameters for the cofactors in PSII have been reported for the CHARMM
potential [2], including of course chlorophyll a.

Good luck,
David

References:
-------------------
1) Matteo Ceccarelli, Piero Procacci, Massimo Marchi
"An ab initio force field for the cofactors of bacterial photosynthesis"
Journal of Computational Chemistry(2003)24(2) 129-142.

2) P. Palencar, F. Vacha, and M. Kuty
"Force field development on pigments of photosystem 2 reaction centre"
Journal Photosynthetica (2005) 43(3) 417-420

On 2/16/08, Sreeja Parameswaran <sreeja.p_at_gmail.com> wrote:
>
> Mathew:
>
> I do have the RESP charges for chl. What I am looking for is some help in
> fixing the missing parameters in my frcmod file (Bond,angle dihedral etc
> related to the Mg-N bonds of the Chl ) from antechamber. Please see parts
> of the frcmod file for details.
>
> MASS
> DU 0.000 0.000 ATTN, need revision
> BOND
> DU-CM 0.00 0.000 ATTN, need revision
> ANGLE
> CD-CM-DU 0.000 0.000 ATTN, need revision
> DU-CM-CT 0.000 0.000 ATTN, need revision
> CM-DU-CM 0.000 0.000 ATTN, need revision
> DIHE
> CD-CM-DU-CM 1 0.000 0.000 0.000 ATTN, need
> revision
> DU-CM-CD-CC 1 0.000 0.000 0.000 ATTN, need
> revision
> DU-CM-CD-CT 1 0.000 0.000 0.000 ATTN, need
> revision
> DU-CM-CT-CT 1 0.000 0.000 0.000 ATTN, need
> revision
> DU-CM-CT-HC 1 0.000 0.000 0.000 ATTN, need
> revision
> DU-CM-CD-HA 1 0.000 0.000 0.000 ATTN, need
> revision
> CM-DU-CM-CT 1 0.000 0.000 0.000 ATTN, need
> revision
> NONBON
> DU 0.0000 0.0000 ATTN, need revision
>
> I am not sure how to fix these missing parameters. Someone recommended I
> could try xleap, but I haven't tried it yet.
>
>
> Thanks
> Sreeja
>
> On Feb 16, 2008 9:09 AM, mathew k varghese <mathew_kvarghese_at_yahoo.co.in>
> wrote:
>
> > Hi Sreeja,
> >
> > Seen your question about parameter generation for chlorophyll. Which
> > Charge method you want to use? RESP? If this is what you require you have
> > to get the Electostatic Potential using some quantum mechanical program like
> > Gaussian. Please look into the tutorial in amber website.
> > http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm
> > You can do a search in amber mailing list regarding antechamber.
> >
> > Regards
> >
> >
> > Mathew
> >
> >
> > /\/\athew
> >
> > Mathew K Varghese
> > Research Scholar
> > School of Pure and Applied Physics
> > M.G.University
> > Kottayam, Kerala
> > India
> >
> > email mathew_kvarghese_at_yahoo.co.in
> >
> >
> > ===========================================================================
> >
> > ------------------------------
> > Did you know? You can CHAT without downloading messenger. Click here<http://in.rd.yahoo.com/tagline_webmessenger_2/*http://in.messenger.yahoo.com/webmessengerpromo.php>
>
>
>
>
> --
> Sreeja Parameswaran
> Department of Physics and Astronomy
> Georgia State University
> 29 Peachtree Center Avenue, Suite 400
> Atlanta, GA 30303
> Phone: 404-324-2939
>

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