From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Tue Nov 02 2010 - 07:38:08 CDT
Hi Christian,
I did the same tutorial yesterday and I think the problem is that the
namd file
uses the setup.psf file for the structure. Change it to the zero.psf you got
using alchemify. This should resolve your problem.
/Markus
Quoting Christian Jorgensen <christian.jorgensen_at_merton.ox.ac.uk>:
> 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
>
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