Missing angle parameters CT3 CT3 CT3

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Mon Nov 01 2010 - 18:12:06 CDT

Hi all, I am going through the FEP tutorial but have encountered a problem.

In section 1.2 (Running the free energy calculation) I run the namd2 forward-noshift.namd > forward-noshift.log simulations but get the following error:

 NAMD FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT3 CT3 CT3

This can suggest a problem with the PSF.

The relevant sections are

 1030 !NATOM
       1 ZERO 1 ZERO CI CT3 -0.270000 12.0110 0
       2 ZERO 1 ZERO HI1 HA 0.090000 1.0080 0
       3 ZERO 1 ZERO HI2 HA 0.090000 1.0080 0
       4 ZERO 1 ZERO HI3 HA 0.090000 1.0080 0
       5 ZERO 1 ZERO CM CT3 -0.270000 12.0110 0
       6 ZERO 1 ZERO HM1 HA 0.090000 1.0080 0
       7 ZERO 1 ZERO HM2 HA 0.090000 1.0080 0
       8 ZERO 1 ZERO HI HA 0.090000 1.0080 0
       9 ZERO 1 ZERO HF HA 0.090000 1.0080 0
      10 ZERO 1 ZERO CF CT3 -0.270000 12.0110 0
      11 ZERO 1 ZERO HF1 HA 0.090000 1.0080 0
      12 ZERO 1 ZERO HF2 HA 0.090000 1.0080 0
      13 ZERO 1 ZERO HF3 HA 0.090000 1.0080 0

For the PDB (the formating looks fine in the PDB file itself)

REMARK original generated coordinate pdb file
ATOM 1 CI ZERO 1 2.419 0.889 -0.515 1.00 0.00 ZERO C
ATOM 2 HI1 ZERO 1 2.947 1.517 -1.265 1.00 0.00 ZERO H
ATOM 3 HI2 ZERO 1 3.259 0.220 -0.228 1.00 0.00 ZERO H
ATOM 4 HI3 ZERO 1 1.668 0.227 -0.997 1.00 0.00 ZERO H
ATOM 5 CM ZERO 1 1.835 1.611 0.701 1.00 0.00 ZERO C
ATOM 6 HM1 ZERO 1 1.097 2.318 0.265 1.00 0.00 ZERO H
ATOM 7 HM2 ZERO 1 2.641 2.107 1.282 1.00 0.00 ZERO H
ATOM 8 HI ZERO 1 1.427 0.890 1.442 1.00 0.00 ZERO H
ATOM 9 HF ZERO 1 2.366 0.983 -0.047 1.00 0.00 ZERO H
ATOM 10 CF ZERO 1 1.180 0.482 1.578 1.00 0.00 ZERO C
ATOM 11 HF1 ZERO 1 1.924 -0.152 2.106 1.00 0.00 ZERO H
ATOM 12 HF2 ZERO 1 0.640 1.039 2.374 1.00 0.00 ZERO H
ATOM 13 HF3 ZERO 1 0.470 -0.218 1.089 1.00 0.00 ZERO H

The supplied zero.top tology file for ethane does not include a section on angles. Could this be the source of the problem?

Thanks

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:21 CST