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

From: Akshay Patny <akshay17.olemiss.edu>
Date: Mon, 29 Jan 2007 10:57:45 -0600

Hi Ross and Amberites

This is the ligand problem I was mentioning about::

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 -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
(JPG picture attached).
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 -1charge approximately).

When I load this liagand (TEL) in leap, it shows me a charge of 0.999960 >>>
----------------------------------------------------------------------------
------------------------------------------------
> charge TEL
Total unperturbed charge: 1.0000
Total perturbed charge: 1.0000
> check TEL
Checking 'TEL'....
WARNING: The unperturbed charge of the unit: 0.999960 is not zero.
Checking parameters for unit 'TEL'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
----------------------------------------------------------------------------
------------------------------------------------

Now shouldn't this have been either -1.0000 or -0.999960 as I expect my
ligand to have a -1 charge and not a +1 charge.

Thanks, can you suggest if I might have did something wrong here?

Akshay Patny (Olemiss)


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Received on Wed Jan 31 2007 - 06:07:23 PST