Re: [AMBER] sulfonamide parameters for correct geometry

From: Annachiara TINIVELLA <>
Date: Thu, 6 Feb 2020 17:17:36 +0100

Dear Junmei,
thank you very much for you answer. I followed your advice and I used QM
methods to optimize the geometry and calculate the charges of the
benzenesulfonamide. I used Jaguar from the Schrodinger suite and I obtained
a similar geometry to the reported 3D geometry of the SO2NH2 group.
Unfortunately, when I tried to use tleap to prepare the topology and
coordinates files to minimize the ligand I obtained the same unrealistic
angles of 94.7 between the sulfur, nitrogen and hydrogen.

To give you more information about the procedure I followed:
1) I used Jaguar to first optimize the geometry of the molecule at
the B3LYP/6-31G** level. PBF was used as the solvent model.
2) I then computed ESP atomic charges through a single point energy
calculation by Jaguar.
3) I saved the output in MOL2 format
4) I generated the corresponding PREP and PDB files using antechamber
(using gaff2 atomtype)
5) I generated the FRCMOD file from the PREP file using parmchk2
6) I generated the TOP and CRD files for minimization using tleap. The
tleap commands were:

source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff2
loadAmberPrep mol.lig_outputJag.prep
loadamberparams frcmod.lig_outputJag
l = loadPDB mol.lig_outputJag.pdb
check l
set default PBRadii mbondi
solvateOct l TIP3PBOX 14.0
saveamberparm l 3ERT_A.outputJag.lig.crd.1
savepdb l 3ERT_A.outputJag.lig.pdb

7) I finally performed 5000 cycles of free minimization using the following
parameters with sander:

  imin = 1,
  maxcyc = 5000,
  ncyc = 1000,
  ntmin = 1,
  ntb = 1,
  ntr = 0,
  cut = 10.0

Both the output of tleap and the output of the minimization had changed the
optimized geometry of the SO2NH2 moiety, with almost 90° angles between S,
N and H atoms.

Could I ask again for your opinion on the matter? Attached you will find
the output of the optimization with Jaguar (outputJag.mol2) and the
minimized sander output (min-outputJag.pdb).

Thank you again for your time and your attention, and please let me know if
you need further information.


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Received on Thu Feb 06 2020 - 08:30:01 PST
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