AMBER Archive (2002)

Subject: Problem with LEAP

From: Miguel de Federico (miguel_at_qorws1.uab.es)
Date: Tue Jul 16 2002 - 05:53:37 CDT

 I'm trying to use tleap for preparing a simple molecule (cyclohexanol)
and I get always the same error. I have revised the structure and seems
OK. Could anybody help me about this?

The error message is as follows:

miguel_at_qorws11 49% tleap -f 05c5axial.leap.in
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.
-f: Source 05c5axial.leap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./05c5axial.leap.in
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/gaff.dat
Loading Prep file: ./c6axial.prep
Bond: Maximum coordination exceeded on .R<c6a 1>.A<C06 6>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<c6a 1>.A<H13 13> .R<c6a 1>.A<C06 6>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 443
!FATAL: Message: bondAtomProblem found
!
!ABORTING.

The leap.in file is:

source leaprc.gaff
loadAmberPrep c6axial.prep
saveoff c6a units2.lib

The prep file is:

    0 0 2

ciclohexanol axial
molecule.res
c5a XYZ 0
CHANGE OMIT DU BEG
  0.0000
   1 DUMM DU M 999.000 999.0 -999.0
.00000
   2 DUMM DU M 999.000 -999.0 999.0
.00000
   3 DUMM DU M -999.000 999.0 999.0
.00000
   4 C01 c3 M 5.021000 4.993000 0.328000
0.243673
   5 C02 c3 M 4.533000 6.372000 -0.149000
-0.019753
   6 C03 c3 M 5.767000 7.299000 -0.042000
-0.018652
   7 C04 c3 M 7.008000 6.365000 -0.085000
-0.018652
   8 C05 c3 M 6.452000 4.929000 -0.236000
-0.019753
   9 O06 oh S 5.077000 5.007000 1.747000
-0.673777
  10 H07 h1 E 4.374000 4.167000 -0.042000
0.012291
  11 H08 hc E 4.206000 6.305000 -1.213000
-0.009364
  12 H09 hc E 3.672000 6.747000 0.448000
0.047121
  13 H10 hc E 5.784000 8.042000 -0.871000
0.004139
  14 H11 hc E 5.746000 7.862000 0.920000
0.013581
  15 H12 hc E 7.687000 6.624000 -0.928000
0.004139
  16 H13 hc E 7.588000 6.456000 0.861000
0.013581
  17 H14 hc E 6.416000 4.653000 -1.315000
-0.009364
  18 H15 hc E 7.085000 4.177000 0.285000
0.047121
  19 H16 ho E 5.230000 4.121000 2.049000
0.383669

LOOP
      C01 C05
IMPROPER

DONE
STOP