FATAL ERROR : Line too long in pdb file

From: amin_at_imtech.res.in
Date: Fri Jun 15 2012 - 19:43:31 CDT

Dear all,
      I am trying to restart my simulation from the restart coor and vel files.
However I keep getting an error like "FATAL ERROR : Line too long in pdb
file". I checked the archives and found that this may be because the coor
file is binary and I may have to add a line bincoordinates and do the same
for velocities. I did this and I was able to restart the simulation.
However, I have a few doubts:
1) Why is a binary restart coor file being written when I have mentioned "binary
output off" in my configuration file?
2)When a simulation run is finished, and the last coor and vel files are
generated, then I am able to restart the simulation with coordinates and
velocities (not bin). However I need to have bincoordinates to restart
simulations from coor and vel files generated at various steps during the run.
3)I learnt from the manual that even when using bincoordinates, I need to have
coordinates line in the configuration file however it will be ignored.
Therefore, I tried to restart the simulation with some random name in the
coordinates line but it complains of not finding the pdb file and works only
when I mention the real file name (ionized.pdb)in the coordinates line.Does that
mean that the original PDB and PSF files are being used to restart and not the
restart.coor file?

Any help will be appreciated.


सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202

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