[gmx-users] Missing Interactions in [ angles ] Section in Topology
Justin A. Lemkul
jalemkul at vt.edu
Mon May 14 23:37:33 CEST 2012
On 5/14/12 5:15 PM, Lara Bunte wrote:
> All needed parameters for [ angles ] in the topology are defined in my .rtp file parametrization and also in the ffbonded.itp in the CHARMM27 folder. This still don't work. In the topology my [ angles ] block looks like
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 19 1
> 1 2 3 1 123.75 250.00
> 1 2 4 1 117.47 230.00
> 3 2 4 1
> 2 4 5 1 115.95 105.00
Well what are these atoms that have missing parameters?
By default, pdb2gmx will generate all possible angles based on bonded
connectivity. Normally, CHARMM27 topologies have type 5 angles (Urey-Bradley)
and the parameters are not explicitly listed. They are looked up from
ffbonded.itp when running grompp.
> So there are lines missing.
> In my ffbonded.itp angles are all defined like
> [ angletypes ]
> ; i j k func th0 cth ub0 cub
> ; f5: Urey-Bradley
> NN3A CN1A ON1 5 123.75 250.00
> NN3A CN1A NN2U 5 117.47 230.00
> CN1A NN2U HN2 5 115.95 105.00
The mismatch here between function type in ffbonded.itp (5) and that which is
present in the topology (1) suggests something is more fundamentally wrong here.
> And in my .rtp file it looks like
> ; Col 1: angle classification
> ; Col 2: equilibrium bond angles in degrees
> ; COl 3: force constant in kcal/(mol*rad^2)
> [ angles ]
> N1 C2 O2 123.75 250.00
> N1 C2 N3 117.47 230.00
> C2 N3 H3 115.95 105.00
> What is the problem? Why are there still this missing lines in the topology?
Perhaps you haven't considered all possible angles. Perhaps there's something
more systemically incorrect in what you've set up. Based on a few snippets of
topology and force field files, unfortunately it's impossible to say at this point.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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