[AMBER] Sulfonamide parameters,

From: loue chen <lauimi.883.gmail.com>
Date: Sun, 3 Nov 2013 14:16:55 +0800

*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 Sat Nov 02 2013 - 23:30:03 PDT
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