AMBER Archive (2007)

Subject: AMBER: calculating charges to modified 4GA unit

From: nag raj (nagaraju_chem_at_yahoo.co.in)
Date: Wed Nov 07 2007 - 05:26:51 CST

Dear Amber Users,
                My system consist of CH3 group in
place of primary and secondary hydroxyl hydrogen atom
of alpha-D-Glucose (Unit name is 4GA in glycam04 force
field of Amber8.0. Primary and secondary hydroxyl
hydrogen atoms in 4GA are replaced by CH3 group). As
per the example given in tutorial
http://amber.scripps.edu/antechamber/efz.html, I
calculated the RESP charges to with and without adding
CH3 group to 4GA unit. The charges of 4GA unit without
adding CH3 group do not match with 4GA unit of
glycam04.

My question is:
 How to calculate the charges to a system consist of
CH3 group in place of primary and secondary hydroxyl
hydrogen atom of alpha-D-Glucose.

       Any suggestion is appriciated.
                   Thank you in advance.

                                 with best regards,
                                  Nagaraja Mulpuri

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu