Re: Missing angle parameters CT3 CT3 CT3

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Nov 01 2010 - 18:52:17 CDT

Topology files don't generally include explicit angles. Every possible angle is generated automatically by psfgen.

I believe this is remedied in NAMD 2.7. Basically, the issue is that an angle is generated that will be removed later in the simulation. However, previous versions of NAMD built the molecule and checked for parameters BEFORE removing any angles/dihedrals that shouldn't exist (because they involve non-interacting groups of atoms in the FEP calculation). The easy hack is to add that angle to the parameter file (par*.inp), just inputting dummy values.

On Nov 1, 2010, at 6:12 PM, Christian Jorgensen wrote:

> 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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