[MMTK] Metalloprotein

Raúl Mera butil_litio at yahoo.com
Tue Jul 26 06:09:11 CEST 2005


Greetings

I have loaded a peptide chain with a zinc atom
complexed in it, using the addGroup() method of the
peptidechain class. My problem is that I can't build a
protein with that peptide because when I try to buld
one with
protein=Protein(chain)
I get this error:

  File "./load_prot.py", line 35, in ?
    sod1_p=Protein(sod1)
  File
"/usr/lib/python2.3/site-packages/MMTK/Proteins.py",
line 597, in __init__
    ss = self._findSSBridges(molecules)
  File
"/usr/lib/python2.3/site-packages/MMTK/Proteins.py",
line 730, in _findSSBridges
    cys = cys + m.residuesOfType('cys') +
m.residuesOfType('cyx')
  File
"/usr/lib/python2.3/site-packages/MMTK/Biopolymers.py",
line 100, in residuesOfType
    if string.lower(r.type.symbol) in types:
AttributeError: 'NoneType' object has no attribute
'symbol'


I tried to build the protein and then add the metal
with addGroup(), but when I use
protein[0].addGroup(...) I get this problem:

"/usr/lib/python2.3/site-packages/MMTK/ChemicalObjects.py",
line 767, in addGroup
    raise ValueError, "bond %s-%s outside object" % \
ValueError: bond AtomCluster ZN-Atom
.chain0.His63.sidechain.N_delta_1 outside object

(I dont get the problem if i use the same command with
a peptide chain so I know the paramethers are all
right)

My question is,: is it posible to build a protein from
a peptide chain with a group? (like the cytochrome-c
which is build in mmtk, but as a peptide chain, not as
a protein)
if  is posible, does somebody know how to do it?
I would pretiate a lot if somebody can help me.

Thanks since now,

Raúl Mera.

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