[MMTK] protein sizes and other stuff

aban@yoda.cm.utexas.edu aban@yoda.cm.utexas.edu
Tue, 9 Nov 1999 22:53:40 -0600

Hi.  I've been attempting to read largish PDB files into
MMTK with no success.  (I'm using 2.0b1 of both MMTK and
ScientificPython.) The code fragment is almost exactly
the one from the examples which preserves atom order:

config = PDBConfiguration('abcd.pdb')
universe = InfiniteUniverse(Amber94ForceField()
universe.addObject(configuration.createAll(None, 1)) 

I've gotten different errors depending on whether or not
I cut the PDB file to make it shorter.  We're talking
about something that's 100+ amino acid residues.  The
PDB file itself is "clean" -- just standard ATOM 
statements of regular amino acids and a couple of TER

Error example: 

Traceback (innermost last):
  File "pdbconstruct.py", line 10, in ?
  File "/usr/lib/python1.5/site-packages/MMTK/PDB.py", line 261, in createAll
    peptide_chains = self.createPeptideChains()
  File "/usr/lib/python1.5/site-packages/MMTK/PDB.py", line 168, in createPeptid
    chain = apply(Proteins.PeptideChain, (chain,), properties)
  File "/usr/lib/python1.5/site-packages/MMTK/Proteins.py", line 237, in __init_
    self._setupChain(circular, properties, conf)
  File "/usr/lib/python1.5/site-packages/MMTK/Biopolymers.py", line 79, in _setu
  File "/usr/lib/python1.5/site-packages/MMTK/PDB.py", line 33, in applyTo
    setResidueConfiguration(residue, self[i], pdbmap[0], altmap)
  File "/usr/lib/python1.5/site-packages/MMTK/PDB.py", line 298, in setResidueCo
    raise IOError, 'Atom '+atom.name+' of PDB residue ' + \
IOError: Atom H of PDB residue LYS not found in residue Lys of object .Lys70

Reading in something an order of magnitude smaller like a 7
residue a.a. chain works fine.  Are there any statically dimensioned
arrays that need to be resized?  (A la 'sizes.h' in the sander
code of Amber.)  I took a glance at the C code in MMTK and it looks
like everything is dynamically malloc'ed...

Some other stuff -- does anyone know how fast MMTK is
is compared to other programs such as sander (in the amber suite)?
I'm interested doing an md run of a 27,000 atom system (with most of 
the atoms being part of water.)  Which leads me to another question:
Does MMTK use the TIP3P water representation?  I haven't been
able to find this anywhere.

Any help is appreciated.


Andrew Ban