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

Abhishek Acharya aacharya at iitk.ac.in
Sun Feb 10 03:50:40 CET 2013

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 ?

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
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

I am very new to gromacs. Kindly help as I'm stuck.
Thanks in advance.
Abhishek Acharya
Structural Biology Lab
Biological Sciences and Bioengineering Department
Indian Institute of Technology Kanpur.

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