AMBER Archive (2007)

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

From: HL Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Fri Feb 02 2007 - 11:40:10 CST

Hullo Akshey

That charge you mention should be -1. as far as I know unless the
residue charge is neutral the charge has to be stated within the resp
input files (for which you'll need to run the resp procedure with it's
constituent programs rather than simply employing antechamber). The
AMBER manual explains these individual resp programs (ie espgen
respgen resp etc) and their corresponding input files.

I hope that helps!

hayden eastwood

Quoting Akshay Patny <akshay17_at_olemiss.edu>:

> Hi 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 -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 lHulload 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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