AMBER Archive (2007)Subject: RE: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Mon Jan 29 2007 - 10:57:45 CST
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)
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|