Hello--
> When I use the pdb2psf program, it converts to a psf file which has
> different name method of the atoms, and the sequence of them is also
> changed. So xplor will complain about atoms cannot find in the
> molecular structure.
Xplor-NIH correctly read the sequence from the PDB file, and created a
PSF, using Xplor-NIH's default atom naming scheme, which differs a bit
from IUPAC. The normal tools for reading structure and coordinate
files in the Python interface will automatically match the
names. Hence,
import protocol
protocol.initStruct('1FKR.psf')
protocol.initCoords('1FKR.pdb')
will match the coordinates to appropriate atoms, and print a bunch of
informational messages in the process. All atoms are matched in this
case.
Simpler, and equivalent would be:
import protocol
protocol.loadPDB('1FKR.pdb')
where the PSF information is automatically generated, such that a psf
file is not needed.
Note that there are sometimes subtle naming issues such that the
improper energy is large- if you run into these, please contact me.
best regards--
Charles
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