Hi!
The attached frcmod file will give you a nice shaped sp3 to you
sulfonamide moiety. I checked it in 2FOU pdb file.
Greeting,
Hector.
> *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
> suggestion.
>
> --
> *Regards,*
> *Tahir Ali Chohan*
> *B.Pharm., M.Phil (Pharm. Chem.)*
> *PhD Scholar*
> *College of Pharmaceutical Sciences*
> *Zhejiang University, Hangzhou, China.*
> *Cell # 0086-13018996850*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
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Received on Mon Nov 04 2013 - 14:30:03 PST
