[MMTK] reading .mol or .sd file

정종영 lisroy at yonsei.ac.kr
Mon Jun 9 03:36:11 UTC 2008


I’m a new user of MMTK to try develop some humble code. 

 

What I want to make is a simple code for minimization of a ligand in the
active site of a receptor protein 

 

The first problem that I face is about reading a ligand file.

 

At first, I referred to an example code about “construction of a DNA
strand with a ligand” in MMTK home page.

 

Referring that code, I was able to load a receptor structure and a ligand
structure into universe object from PDB file. 

 

But in this case, a ligand was written in .pdb file. And after reading a
ligand and a receptor, I tried to minimize this universe containing a
receptor and a ligand. In this step, sometimes “AttributeError” was
occurred.

 

AttributeError: AtomType instance has no attribute ‘amber_atom_type’

 

How do I get molecular contents from .mol or .sd files using MMTK?

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