Re: [modeller_usage] symmetry and molecular dynamics
To: JEAN WATERMEYER <>
Subject: Re: [modeller_usage] symmetry and molecular dynamics
From: Modeller Caretaker <>
Date: Fri, 28 Mar 2008 18:42:22 -0700
JEAN WATERMEYER wrote:
We are trying to build a homotetramer model but having some difficulty
maintaining symmetry. I've read the previous posts but maybe someone
can help me further - I'm new to Modeller and to Python.
It's hard to tell from the code snippet. It looks correct (I'm assuming
this code is from the special_restraints method?) but maybe you're not
using the class properly elsewhere in the script - can you post your
complete script? The most common mistake is to derive a 'mymodel' class
from 'automodel' but then to instantiate a regular 'automodel' object
rather than the new 'mymodel', in which case any additional restraints,
patches etc. in 'mymodel' are not applied.
We can think of a few ways to get around this:
1) do no molecular dynamics, only minimisation (maybe someone can tell
Sure, you can set automodel.md_level to None, which will turn off the MD
refinement part. But if MD is not maintaining the symmetry, it seems
unlikely to me that CG minimization would. It is more likely that
there's a problem with your energy function.
2) run molecular dynamics only on selected regions of the model so that
the core remains fixed in place (again, how would I do this?)