Francesco Oteri wrote:
ffbonded.itp is right, grompp misses only a particular dihedral.
Everithing is fine for bond, angle and some dihedrals.
What exactly means "zeroing out all terms for the unknown dihedrals"? It
means that are not present in tpr or that parameters (i.e reference
angle, multiplicity,...)
are zero?
The parameters are set to zero.
-Justin
Il 21/11/2011 21:21, Justin A. Lemkul ha scritto:
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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