This is the command i execute:
ambpdb -p example.tpp <example.rsmd> example.pdb
and this is what appears in example.pdb
NATOM or NRES is too big:
NATOM = 165868; max is 150000
NRES = 49825; max is 50000
I don't know if the failure is in the way i execute ambpdb. And it's
true. The problem with residue number is with ptraj. Sorry.
Thanks
El jue, 07-01-2010 a las 10:29 -0500, case escribió:
> 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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--
Fernando Martín García.
Centro de Biología Molecular "Severo Ochoa".
C/ Nicolás Cabrera, 1.
Campus UAM. Cantoblanco, 28049 Madrid. Spain.
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Received on Thu Jan 07 2010 - 08:00:05 PST
