Hello Tahir,
Benzenesulfonamide, with a molecular charge of zero, is in Wolf2Pack database. This includes HF/6-31G(d) relative potential energy curves for all bonds (4 total), angles (6 total), and torsion angles (2 total) associated with the sulfanamide group (i.e. 167 QM data points for MM comparison). Benzene also exists for getting access to the QM data points for that part of your parent molecule.
I would suggest testing the output of antechamber using Wolf2Pack to see how well the molecular mechanics potential energy curves match the QM derived curves. You can copy and past antechamber's frcmod file in the force-field box (located in the last step of W2P's workflow). Make sure that the atom types that antechamber assigns are used in benzenesulfonamide (ie. Atom Typing step in W2P's workflow) prior to testing the frcmod file.
You will be able to test both parm99SB and gaff atom types, as well as their assigned parameters. If you need to optimized any parameters, W2P will allow you to do this as well by directly adjusting the terms in the frcmod file.
Best Regards,
Karl
----- Original Message -----
From: "loue chen" <lauimi.883.gmail.com>
To: amber.ambermd.org
Sent: Thursday, July 25, 2013 7:04:59 PM
Subject: [AMBER] Amber force field for Benzene sulfonamide.
Dear all,
I am interested in molecular dynamics simulation with small molecule and
protein to explore selectivity mechanism. But unfortunately I have
encountered some problem and I need help.
1). The ligand I am using, contains Benzene sulfonamide group.
2). I found that Amber force field parameters for this particular group are
missing.
3). I tried to use prmcheck in order to use default force field but the
results were not satisfactory.
4). During my search on google I got prmtop file at the following link (
http://archive.ambermd.org/200806/0257.html)but I don’t know how to
transfer these parameters to forcmod.
So I need help to get the force field file for this group (Benzene
sulfonamide). I will be grateful for this favor.
--
*Regards,*
*Tahir Ali Chohan*
*B.Pharm., M.Phil (Pharm. Chem.)*
*PhD Scholar*
*College of Pharmaceutical Sciences*
*Zhejiang University, Hangzhou, China.*
*Cell # 0086-13018996850*
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Received on Fri Jul 26 2013 - 04:30:03 PDT
