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Hello Ramon--
>
> I get stuck quite in the beginning. When I read the standard nucleic.par
> and nucleic.top, the program complains about duplicate definitions of
> parameters.
>
>
> import protocol, ivm
> protocol.initRandomSeed(1)
>
> #Define topology and subsequent parameters
> protocol.initTopology('/home/ramon/COMPROG/xplor-nih-2.18/toppar/nucleic.top')
> protocol.initParams('/home/ramon/COMPROG/xplor-nih-2.18/toppar/nucleic.par')
>
If you're running /home/ramon/COMPROG/xplor-nih-2.18/bin/xplor
then these files are read in by default when it is determined (within
loadPDB) that your structure is a nucleic acid. i.e. you don't need
these lines. You can specify the string "nucleic" in both cases- it
specifies using default topology/parameter files (the ones you're
loading). You can change the default parameter/topology files using
import protocol
protocol.paramters["nucleic"] = "/path/to/other/params"
protocol.topology["nucleic"] = "/path/to/other/topo"
> # Read PDB and generate PSF on the fly and initializes coordinates
> protocol.loadPDB('par/ED_53_acc.pdb')
>
When you use loadPDB, you don't need to specify initTopology/Params. The
caveat is that nonstandard residues can't be handled without some other
work.
And you're right- the documentation should be improved.
best regarads--
Charles
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