AMBER Archive (2002)

Subject: Dummy torsions

From: Aldo Jongejan (jongejan_at_chem.vu.nl)
Date: Tue Oct 15 2002 - 08:33:02 CDT


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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