Closed GoogleCodeExporter closed 8 years ago
Original comment by christop...@gmail.com
on 6 Sep 2013 at 9:22
I think this is one of the first things to do on the way to NAMD support.
Original comment by christop...@gmail.com
on 4 Dec 2013 at 2:26
With the upcoming gromacs 5.0 release this get even more urgent.
Sikandar can you have a look at this? The xyzreader and the pdbwriter should
be a good starting point.
Original comment by jungh...@votca.org
on 12 Dec 2013 at 7:10
Sure, Christoph, I will start looking into it.
Original comment by symasha...@gmail.com
on 12 Dec 2013 at 7:14
The (stupid) pdb,xyz, and gro parsers already exist in votca-ctp. If you want
to make readers out of it i can send you the code.
Original comment by andrienko@googlemail.com
on 12 Dec 2013 at 9:05
This seems ctp_map uses CSG::TrajectoryWriter, CSG::TrajectoryReader and
CSG::TopologyReader.
Original comment by christop...@gmail.com
on 12 Dec 2013 at 9:27
yes, ctp_map relies on CSG reader and writer, but many objects in the libctp
have their own readers/writers, mostly for test purposes. this is a 50 lines
code if you don't want to have it 100% user-safe. There was no sense to change
ctp_map (we considered this) since the Topology reader is essential there -
rewriting it would be a pain.
Original comment by andrienko@googlemail.com
on 12 Dec 2013 at 9:47
PDB2Map::readPDB from src/libctp/tools/pdb2map.h looks good. I copied some
parts to a new pdbwriter. Right now this code will only be compile with
-DWITH_GMX=OFF and it fail from multi-frame pdb files.
Original comment by christop...@gmail.com
on 12 Dec 2013 at 11:54
I fixed reading of multi-frame pdb files. When reading a pdb trajectory written
by csg_map, I realized that our pdb writer is actually not 100% correct, it
writes the charges in the wrong column, so I didn't implement reading charges
in the reader either.
Denis, do you make use of the charges in csg_map?
Original comment by christop...@gmail.com
on 16 Dec 2013 at 4:37
Nope, we read charges from mps files (distributed multipoles) - force-field
charges make no sense for evaluating electrostatic energies only. No need
to have them in the pdb.
Original comment by andrienko@googlemail.com
on 16 Dec 2013 at 5:49
Great, in csg charges aren't use either and there is a warning to make the user
aware.
Sikandar/Victor, please review my code and if you feel it is good enough,
please close this issue.
Original comment by christop...@gmail.com
on 16 Dec 2013 at 5:58
Original comment by christop...@gmail.com
on 1 Jul 2015 at 11:21
Original issue reported on code.google.com by
christop...@gmail.com
on 6 Sep 2013 at 9:01