Re: [AMBER] Sulfonamide parameters,

From: Karl N. Kirschner <>
Date: Mon, 4 Nov 2013 15:12:06 +0100 (CET)

Hi Loue Chen (or Tahir Ali Chohan?),

  From your email, it appears that the only problem you are having is getting your force field to reproduce reasonable angles for H-N-S and N-S-O. As you know from our previous conversation, Wolf2Pack has benzenesulonamide is its database, with QM data computed many of its internal coordinates, including the H-N-S and N-S-O angles. According to my HF/6-31G(d) optimized conformation, H-N-S and N-S-O should have values close to 111 and 106 degrees.

  You can use W2P see how AMBER's major force fields perform in reproducing the QM target data for this molecule. You can also optimize the parameters that you are questioning/concerned with. For instance, you could start by coping and pasting Antechamber's frcmod file into the last workflow step of W2P, see how the existing parameters reproduce the QM data, and then adjust accordingly.

As far as your partial atomic charges look, all I can say is that they look reasonable based on the fact that the symmetrically equivalent atoms have the same charge values. However, if you haven't already done so, I would suggest looking at the R.E.D. website for generating partial atomic charges that are compatible with the gaff/parm99SB force fields.

Best regards,

----- Original Message -----
From: "loue chen" <>
Sent: Sunday, November 3, 2013 7:16:55 AM
Subject: [AMBER] Sulfonamide parameters,

*Dear experts,*

  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) As I perform the energy minimization the angles of the H-N-S and N-S-O
bonds becomes unnatural, both of which are a little over 90 degrees.

3) I am using the following method for calculation of charges of my ligands
(p hf/6-31g(d) pop=mk iop(6/33=2).

During my search on Google I found that some other people also have been
suffered with the same problem and finally they solved it by making some
modification in their input files.

So I need help to fix out this problem.

 I will be grateful for this favor.
Here I am attaching original PDB of my ligand, Mol2 file, PDB after energy
minimization (min3) and frcmod file. So that you can give me batter

*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 Mon Nov 04 2013 - 06:30:02 PST
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