Francesco Oteri wrote:
I am using parameters already developed for CHARMM. So I guess the
parameters are right and I am sure there is no error in the trasformation
from CHARMM to GROMACS format. May the option "-zero" in grompp solve my
problem?
Well, using "grompp -zero" will bypass the error by zeroing out all terms for
the unknown dihedrals. If there are 96 of them, that means you will have
completely incorrect bonded interactions.
If you have parameters that should work for this particular molecule, they are
not being found in ffbonded.itp. That's the problem. So you can resolve the
problem by adding bonded parameters to that file or defining them locally in
your .top with a suitably placed [dihedrals] (or whatever else) directive.
-Justin
Il 21/11/2011 21:00, Justin A. Lemkul ha scritto:
francesco oteri wrote:
Dear gromacs users,
I am trying to build the topology for a protein-ligands system. When
I run grompp I obtain 96 of the following errors:
ERROR 1 [file topol_Protein_chain_S.itp, line 38658]:
No default Proper Dih. types
The errors correctly says that dihedral parameters are missing for my
ligands. My question is, there is a method to avoid considering such
a dihedrals, avoiding topology editing?
In other words, I don't wanna edit the .top file removing by-hand the
lines generating the error.
If you're missing parameters, you need to assign them. Whether or not
that requires deriving new dihedral types depends on the complexity of
the molecule.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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