AMBER Archive (2008)

Subject: Re: AMBER: AMBER parameters for Chlorophyll

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Sat Feb 16 2008 - 08:09:30 CST

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

Sreeja Parameswaran <sreeja.p_at_gmail.com> wrote: Hi!
  
 I am trying to obtain AMBER parametrs for chlorophyll a. I used Antechamber to get the force field parameters. But some parameters, connected to the Mg atom (antechamber assignes AMBER atom type as DU), are missing.
   
 These are the missing parameters in my frcmod file.
  
 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 would greatly appreciate any help in obtaining these missing parameters.
  
 Thank You
 Sreeja 

-- 
Sreeja Parameswaran
Department of Physics and Astronomy
Georgia State University
29 Peachtree Center Avenue, Suite 400
Atlanta, GA 30303
Phone: 404-324-2939

 

/\/\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

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