AMBER Archive (2007)

Subject: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Fri Jan 19 2007 - 02:34:58 CST

Dear Amberites

I have calculated charges using RESP procedure in
antechamber for one of my ligands: Telmisartan. The ligand
contains a carboxylate moiety which I want to keep charged
while simulation, so I defined formal -1 charge during
gaussian job.

I derived the PREP file for the ligand using RESP which is
Telmisartan_charged_resp.prep. I then converted this into a
MOL2 file using

% antechamber -rn TEL -fi prepi -i
Telmisartan_charged_resp.prep -fo mol2 -o
Telmisartan_charged_resp_ante.mol2

I then looked into the Telmisartan_charged_resp_ante.mol2
file for charges.
Following are the RESP derived charges for certain atoms >>>

Carboxylate Carbon (C32) > 0.9513
1st Carboxylate Oxygen (01) > - 0.8119
2nd Carboxylate Oxygen (02) > - 0.8119

Please suggest me if these charges look reasonable for
charged carboxylate moiety (it does add to a formal -1
charge approximately).

Thanks, I look forward to hear from you.

Akshay Patny (Olemiss)

Akshay Patny
(Graduate Student @ PhD)
Department of Medicinal Chemistry
School of Pharmacy, University of Mississippi
417, Faser Hall, University, MS - 38677
Tel : 662-915-1286(Off.)
E-mail : akshay17_at_olemiss.edu
Web : www.olemiss.edu



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