AMBER Archive (2003)

Subject: AMBER: antechamber problem

From: Qiang Lu (qiangl_at_uci.edu)
Date: Wed Aug 20 2003 - 13:56:14 CDT

Hi Junmei

When I convert from pdb to prepin file, it only convert 18 atoms, other
22 are labeled X like follow
I think I need to increase the limit of antechamber, could you please
tell me how to do it.

Thank you

    0 0 2

This is a remark line
molecule.res
ZNF INT 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 CA c3 M 3 2 1 1.540 111.208 180.000 0.00000
   5 HA1 hc E 4 3 2 1.100 66.252 -37.576 0.00000
   6 HA2 hc E 4 3 2 1.100 70.295 -170.274 0.00000
   7 HA3 hc E 4 3 2 1.100 83.107 68.228 0.00000
   8 CB c3 M 4 3 2 1.526 169.477 -70.720 0.00000
   9 HB2 hc E 8 4 3 1.090 109.520 -155.561 0.00000
  10 HB3 hc E 8 4 3 1.091 109.484 -35.623 0.00000
  11 CG c2 M 8 4 3 1.509 115.012 84.373 0.00000
  12 ND1 n2 M 11 8 4 1.404 122.000 -179.982 0.00000
  13 CE1 c2 M 12 11 8 1.329 107.677 -179.994 0.00000
  14 HE1 h5 E 13 12 11 1.090 119.989 -179.997 0.00000
  15 NE2 na M 13 12 11 1.310 108.994 0.016 0.00000
  16 HE2 hn E 15 13 12 1.010 124.760 -179.940 0.00000
  17 CD2 c2 M 15 13 12 1.367 110.298 -0.043 0.00000
  18 HD2 h4 E 17 15 13 1.089 119.977 179.972 0.00000
  19 X 1 0 1 8.221 nan 942.009 0.00000
  20 X 1 0 1 8.221 nan 942.009 0.00000
  21 X 1 0 1 8.221 nan 942.009 0.00000
  22 X 1 0 1 8.221 nan 942.009 0.00000
  23 X 1 0 1 8.221 nan 942.009 0.00000
  24 X 1 0 1 8.221 nan 942.009 0.00000
  25 X 1 0 1 8.221 nan 942.009 0.00000
  26 X 1 0 1 8.221 nan 942.009 0.00000
  27 X 1 0 1 8.221 nan 942.009 0.00000
  28 X 1 0 1 8.221 nan 942.009 0.00000
  29 X 1 0 1 8.221 nan 942.009 0.00000
  30 X 1 0 1 8.221 nan 942.009 0.00000
.......

Qiang Lu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu