On Thu, Jan 07, 2010, Fernando Martín García wrote:
> I'm using ptraj because ambpdb fail for big systems
Can you give details of how ambpdb is failing? We've used for systems
of more than 400,000 atoms, but of course the details may be important.
[It does give "***" for atom numbers, not for residue numbers. This is not
a problem for our applications, but will be fixed in the next release.]
But getting reproducible reports of failures helps us fix problems.
Aside: be *very* careful if you follow Jason's advice about changing the
formats of PDB files. There actually is no good way to put large systems
into PDB format -- the specification allows only 5 digits for the atom
sequence number, and 4 digits for the residue sequence number. We just
"cheat" by starting over at 0 when the number gets to be too big to fit.
...thx...dac
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Received on Thu Jan 07 2010 - 07:30:04 PST
