AMBER Archive (2002)

Subject: sulfonic group generated with antechamber

From: Michael Jakusch (michael.jakusch_at_pharma.anbi.ethz.ch)
Date: Thu Jul 25 2002 - 07:23:30 CDT

Hi everybody!

A colleague of mine has a problem with a ligand that he parameterized
using antechamber. The molecule contains a sulfonic group attached to
an aliphatic sidechain (see the prep and frcmod files below). During
the first steps of the simulation the structure of the sulfonic group
distorts heavily and the (S-O-H) proton bumps into the neighboring
(S=O) oxygen.

Any hints?

Michael

* The prep file:
---------------

    0 0 2

This is a remark line
molecule.res
EPE XYZ 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 O8 oh M 3 2 1 1.540 111.208 180.000 -0.608
   5 H13 ho E 4 3 2 0.950 88.613 -104.636 0.401
   6 C8 c3 M 4 3 2 1.424 21.025 82.124 0.128
   7 H11 h1 E 6 4 3 1.099 109.411 -52.803 0.024
   8 H12 h1 E 6 4 3 1.101 109.404 67.130 0.041
   9 C7 c3 M 6 4 3 1.540 109.683 -172.825 0.168
  10 H9 h1 E 9 6 4 1.100 107.605 46.845 0.038
  11 H10 h1 E 9 6 4 1.100 107.636 164.768 0.051
  12 N4 n3 M 9 6 4 1.503 116.726 -74.196 -0.729
  13 C5 c3 3 12 9 6 1.476 108.299 76.704 0.163
  14 C6 c3 B 13 12 9 1.492 111.697 -167.761 0.169
  15 H7 h1 E 14 13 12 1.100 110.073 55.368 0.020
  16 H8 h1 E 14 13 12 1.100 110.093 176.141 0.056
  17 H5 h1 E 13 12 9 1.100 108.901 71.928 0.031
  18 H6 h1 E 13 12 9 1.100 108.900 -47.454 0.072
  19 C3 c3 M 12 9 6 1.503 114.419 -162.766 0.165
  20 H3 h1 E 19 12 9 1.100 110.326 -61.769 0.030
  21 H4 h1 E 19 12 9 1.100 110.340 59.280 0.050
  22 C2 c3 M 19 12 9 1.538 106.000 178.745 0.171
  23 H1 h1 E 22 19 12 1.100 108.657 177.404 0.051
  24 H2 h1 E 22 19 12 1.100 108.648 -63.542 0.024
  25 N1 n3 M 22 19 12 1.527 112.638 56.925 -0.728
  26 C9 c3 M 25 22 19 1.496 113.959 -178.883 0.212
  27 H14 h1 E 26 25 22 1.099 107.547 -120.454 0.067
  28 H15 h1 E 26 25 22 1.100 107.529 121.745 0.071
  29 C10 c3 M 26 25 22 1.506 117.047 0.642 -0.405
  30 H16 h1 E 29 26 25 1.100 108.454 107.797 0.136
  31 H17 h1 E 29 26 25 1.100 108.457 -11.043 0.125
  32 S s6 M 29 26 25 1.772 113.518 -131.618 1.617
  33 O2S o E 32 29 26 1.462 104.577 71.423 -0.684
  34 O3S oh S 32 29 26 1.513 110.104 -36.956 -0.762
  35 H18 ho E 34 32 29 0.950 109.481 179.970 0.484
  36 O1S o M 32 29 26 1.472 106.748 -157.641 -0.647

LOOP
   N1 C6

IMPROPER

DONE
STOP
---------------

* The prep file:
---------------
remark goes here
MASS

BOND

ANGLE
c3-c3-s6 72.669 110.615 Calculated with empirical approach
c3-s6-oh 39.850 102.630 Calculated with empirical approach

DIHE

IMPROPER

NONBON
--------------- 

-- 
Dr. Michael Jakusch

ETH - Swiss Federal Institute of Technology
Department of Applied Biosciences
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
Phone: +41.1.635 60 71
Fax:   +41.1.635 68 84
email: michael.jakusch_at_pharma.anbi.ethz.ch