Hi all,
I have a problem defining the dummy torsion
parameters needed to let a molecule dissapear
(following the methanol-in-solvent-box tutorial)
Methanol has no torsions, but my molecule has..
Anyway, xleap xomplains about missing torsion
parameters:
> saveamberparmpert tmp model_H2X.top model_H2X.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: 16.998200 is not zero.
WARNING: The perturbed charge: 16.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
*** Proper torsion parameters missing ***
atom names: HE1-CE1-NE2-CD2
atom types: H5-CR-NA-CW =pert=> DH5-DCR-DNA-DCW
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
- e.g. DH5-DCR-DNA-DCW 1 0.0 0. 2.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
etc.
If you add this suggested torsion setting to a .frcmod file
it will still give you the errors!!
DIHE
DH5-DCR-DNA-DCW 1 0.0 0. 2.
On the web, I could only find, that the latter should work, but
I can nowhere find that it really works!!
Does anybody has an example on how to do this?!
with kind regards,
aldo
PS: you can see that all other parameters are read in just fine!
It should offcourse be relatively simple to build a kind of
'shadow' file for all the atomtypes, by just copying the .dat file
and add 'D' (for dummy). But probably, somewhere you just exceed
the space given to a certain variable and it will fail :-)
--
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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands
e-mail: jongejan_at_chem.vu.nl
tlf: +31 (0)20 4447612
fax: +31 (0)20 4447610
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Received on Tue Oct 15 2002 - 06:33:02 PDT
