[gmx-users] Missing Interactions in [ angles ] Section in Topology

[Justin A. Lemkul]

On 5/14/12 5:15 PM, Lara Bunte wrote:
> Hi
>
> 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

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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