[MMTK] MD with fixed atoms

Victor Muñoz chewaka.87 at gmail.com
Fri May 6 06:27:31 UTC 2011

The error appears when I run that command:

trajectory = Trajectory(self.universe, "dynamics.nc", "w", "MD test")

Where the self.universe is the universe created by Chimera for the MMTK. I
have put a print statement before the crash happens in _typename:

print self.type

The self.type when it crashes is None.

I'm using Ubuntu right now.

Thanks for your help.

2011/5/5 Konrad Hinsen <research at khinsen.fastmail.net>

> On 5 May 2011, at 23:18, Victor Muñoz wrote:
>  Problem fixed. I just used the VelocityVerletIntegrator() instead of
>> writing it like in the MD integrator in python example. This way the
>> universe keeps updating and I can mantain fixed the atoms I want.
> Now I understand what went wrong: every integrator and minizer has to know
> about fixed atoms and handle them specificlly. VelocityVerletIntegrator
> does, the Python example doesn't, because I wanted to keep it as simple as
> possible.
>  Now I have other problem when I try to save the MD. When I run the
>> Trajectory() script in the MMTK, I get the error 'NoneType' object has no
>> attribute 'name' in :
>> File
>> "/home/victor/bin/chimera_1.5.2/lib/python2.7/site-packages/MMTK/ChemicalObjects.py",
>> line 486, in _typeName
>>    return self.type.name
> Which script exactly are you running? And what is your system? The error
> message points to some problem with identifying some object in your
> universe.
>  I'm trying to save the dynamics into the netCDF format using the universe
>> created by the UCSF chimera, as the dynamics already works. But neither
>> Conrad nor I knows which type do we need in order for Trajectory() to work.
> Can you check (and tell me) what "self.type" is when the crash happens? You
> can find out quickly using a debugger such as pdb.
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: research at  khinsen dot fastmail dot net
> ---------------------------------------------------------------------

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