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

Lara Bunte lara.bunte at yahoo.de
Wed Mar 7 18:19:19 CET 2012

Hi Justin

I am using a CHARMM27 force field. I create a pdb file with the coordinates of my molecule and I create a .rtp and a .hdb file for this. I also edit atomtypes.atp, ffnonbonded.itp and residuetypes.dat

The parameters for the parametrization are out of a supporting information of a paper that did MD with my molecule. 

The System is my molecule (isoalloxazine) in water. 

Do you want to see my .rtp file?

Thanks you for helping me.


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 20:34 Dienstag, 6.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

Lara Bunte wrote:
> Hi
> In some lines the equilibrium angle and the force constant is missing.I give you an example:
> The [ angles ] section is build like
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>    2     1    19     1    123.75     250.00
>     1     2    3      1    123.75     250.00
>     1     2    4      1    117.47     230.00
> And my pdb2gmx output is for example something like
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>     2     1    19     1    123.75     250.00
>     1     2     3      1  
>     1     2     4      1    117.47     230.00

So you have a complete topology and one that has missing parameters, or are you adapting an incomplete topology?

What force field are you using?  What is the system?  For a normal protein system, most force fields (all except Gromos, if I recall) produce bonded directives with no parameters; they are looked up from ffbonded.itp and not stated explicitly, so "missing" parameters are completely normal and not problematic.  If you're dealing with something nonstandard and you've had to create .rtp entries, you'll need to post that information for diagnostic purposes.

In principle, there's nothing wrong with any of this.  The blank lines will be filled in with existing parameters from [angletypes] in ffbonded.itp.  These parameters are only overwritten if explicitly present in the topology.  If there is a bonded interaction referenced in the topology that does not exist in ffbonded.itp, grompp will fail with a fatal error.


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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