AMBER Archive (2008)

Subject: Re: AMBER: AMBER parameters for Chlorophyll

From: Sreeja Parameswaran (sreeja.p_at_gmail.com)
Date: Sat Feb 16 2008 - 08:45:32 CST

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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