IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Topology/parameter files for glycerol?

Kurt S. Thorn ksthorn at flagstaff.princeton.edu
Wed Apr 17 12:36:44 EST 1996


Could somebody send me working topology/parameter files for glycerol, or
explain to me why mine don't work?  The error I get is when hbuild reaches
the glycerol; it says:
 %CODDIH-ERR: no dihedral parameters for CH2E CH1E OH1  H

This is despite teh fact that there is the line
dihe X    CH1E OH1  X    1.5       3       0.0! CHANGED TO ROUGHLY MEOH
in parhcsdx.pro.  If I explicitly add the line for CH2E CH1E OH1 H,
it doesn't help.

Here are my files:



  ATOM C1   TYPE=CH2E   CHARge= 0.25   END  !#
  ATOM O1   TYPE=OH1   CHARge=-0.65   END  !#
  ATOM C2   TYPE=CH1E   CHARge= 0.25   END  !#
  ATOM O2   TYPE=OH1   CHARge=-0.65   END  !#
  ATOM C3   TYPE=CH2E   CHARge= 0.25   END  !#
  ATOM O3   TYPE=OH1   CHARge=-0.65   END  !#
  ATOM H1   TYPE=H     CHARge= 0.40   END  !#
  ATOM H2   TYPE=H     CHARge= 0.40   END  !#
  ATOM H3   TYPE=H     CHARge= 0.40   END  !#

 BOND O1   C1
 BOND C1   C2
 BOND C2   C3
 BOND C3   O3
 BOND C2   O2
 BOND O1   H1
 BOND O2   H2
 BOND O3   H3

 DIHEdral  H1   O1   C1   C2  !FROM THR
 DIHEdral  O1   C1   C2   O2  !FROM THR
 DIHEdral  C1   C2   O2   H2  !FROM THR
 DIHEdral  C1   C2   O2   H2  !FROM THR
 DIHEdral  C2   C3   O3   H3  !FROM THR

 IMPRoper  C2   C1   O2   C3  ! chirality or flatness improper   -35.50

 DONOr H1 O1
 DONOr H2 O2
 DONOr H3 O3
 ACCEptor O1 C1
 ACCEptor O2 C2
 ACCEptor O3 C3


and parameters:

angle CH2E  CH1E  CH2E   672.465  110.400 !1.7
angle CH2E  CH1E  OH1   485.856  111.100 !2.0


     Kurt Thorn - ksthorn at princeton.edu - http://www.princeton.edu/~ksthorn
"Do not
 - dangle the mouse by its cable or throw the mouse at co-workers."
-- From the Indigo2 Workstation Owner's Guide

More information about the X-plor mailing list

Send comments to us at archive@iubioarchive.bio.net