Hi all,
I modified the 1JFF structure from pdb.org using Acclerys, and saved the
structure as a pdb file. I then loaded the file into leap and tried to
generate the prmtop and inpcrd file but i was getting "FATAL" errors when I
tried to save. So I figured it was because there were some parameters
missing or LEaP wasn't recognizing some of the atoms. Then I tried to follow
the steps on this tutorial to try and use antechamber to fix the pdb file,
but I got more errors.
Warning: detected more than 10 Residue sequence numbers;
this may be a large multiple residue PDB file;
large multiple residue PDB files are not supported.
Continuing, but problems may be encountered.
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Error: cannot run "/home/matthew/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
[matthew.matt-pc octMD]$
I got the initial "warning" message many many times. If anyone knows if
there is something that must be done for large pdb files or if anyone knows
of a good antechamber tutorial, please let me know.
Sincerely,
Matt Antalek
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Received on Sat Oct 29 2011 - 15:00:03 PDT
