Hi Matt,
Antechamber is designed to derive charges for a small ligand that docks in
a protein, not an entire protein. It runs a semi-empirical quantum
mechanical calculation to determine the charge density around the molecule,
and then fits partial charges to match that electrostatic potential, more
or less. QM calculations are quite expensive, and they're never run on
full proteins to determine charges. They're run on small compounds and
single amino acid/nucleic acid residues to define charges for that residue,
which are then used on full proteins. As the error message suggests,
antechamber will not work for full proteins, as that's not what it was
designed for.
My guess is that Accelrys messed up some of the atom and/or residue naming
in your PDB which prevents leap from recognizing your structure. The only
time you should need to run antechamber (or get other parameters) is when
you have non-standard amino acids or other small organic molecules in your
structure. All other residues (standard amino acids and nucleic acid
residues) should have their parameters already defined in existing
parameter sets (including parameters and partial charges).
If you print out the full error you're getting on the first step, we may be
able to help more.
HTH,
Jason
On Sat, Oct 29, 2011 at 5:51 PM, Matthew D Antalek
<mantale1.binghamton.edu>wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Oct 29 2011 - 15:30:02 PDT
