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[ESPResSo-users] Missing atoms during writepdb or blockchain

Subject: [ESPResSo-users] Missing atoms during writepdb or blockchain
Date: Fri, 16 Dec 2016 21:09:25 +0000

Dear users,

I am currently on the latest master branch using the Tcl interface. I am facing a rather peculiar problem. I have been running peptideB with no issues:

Everything runs as expected and all .pdb output from peptideB are correct. However, if I attempt to write an output using Espresso's writepdb or blockfile, I get missing atoms in the file. For instance if my system has 150 atoms, the output gives me only 100 atoms. 

Moreover, if I try to add interactions, for example with "part 1234 bond 40 5678", I get errors of "set all partner atoms first" which clearly implies the particles are not there at all. Is there any situation at all where the particles have been defined but somehow gets truncated somewhere?

Best Regards,
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