[gmx-users] Removing errors related to missing dihedrals.

Justin Lemkul jalemkul at vt.edu
Sun Feb 10 20:43:49 CET 2013

On 2/9/13 9:50 PM, Abhishek Acharya wrote:
> Dear Gromacs Users.
> I generated a topology file of GDP for OPLSAA force field using MKTOP. But
> on running grompp I got a list of No default Angle types and No default
> Ryckaert Bell. types error. So this time i manually assigned the
> appropriate atom types by looking up the atomtypes.atp file and managed to
> come down from 24 errors to 9 errors. All the errors correspond to missing
> dihedrals only. I notice that these missing dihedrals are concentrated
> around two specific region of the structures which are the Pyramidine ring
> of Guanine and the bond connecting the C1 atom of ribose and N9 atom of
> the imidazole ring of Guanine.
> So i have a two part query:
> 1. I had assigned the atom types for the Guanine part of GDP from the
> already defined atom types for Guanine in the library. Is it not then
> surprising to get 6 missing dihedrals for the pyramidine ring considering
> the fact that Guanine is already parameterized ? Am i wrong in this ?

The OPLS-AA implementation is a bit of a hodgepodge of collected parameters. 
The atomtypes are indeed present, but probably a lot of bonded parameters are 
missing, as there are not even any official .rtp entries for nucleotides.

> 2. In an effort to remove the missing dihedral errors related to the C1-N9
> region it tried to manually add the missing diherals to the ffbonded.itp
> file.
> I noticed one of the missing dihedral was: OH-CT-CT-NA (O2'-C2'-C1'-N9).
>   So i added the dihedral entry as:
> NA     CT     CT     OH      3     16.73600 -16.73600   0.00000   0.00000
>   0.00000   0.00000
>   based on an already defined dihedral:
> NT     CT     CT     OH      3     16.73600 -16.73600   0.00000   0.00000
>   0.00000   0.00000.
> But the error corresponding to this dihedral remained on re-run.
> Is there anything wrong with this ? Do i need to edit some other related
> files.

If I'm reading the atomtypes.atp file correctly, you should be using opls_354B 
(N*) rather than opls_354 (NA).  I would surmise that opls_354 is for use in 
isolated guanine, not the nucleoside/nucleotide forms.  In either case, 
theoretically your method works fine for adding missing parameters.  If it's 
still not working, then you're not adding the right parameters.  If you need 
help doing this, you need to provide relevant topology sections and actual 
screen output.



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


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