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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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