From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Mon Sep 09 2013 - 04:15:06 CDT

Hi,

I'm building a modified version of the AutoIMD plugin to add MDFF forces to the simulation. I hope to use this in interactive (re-) fitting of structures where the electron density map is ambiguous or where errors have been made in threading. It's working, but I'd like to be able to add cispeptide and/or chirality restraints as necessary. I see that the AutoIMD script has existing code for this:

cispeptide extrab ...
chirality extrab ...

but this is specifically designed for when AutoIMD is called from within the cispeptide or chirality plugins. When I force it, these crash looking for variables that haven't been set. I'm wondering if this will be easy to hack, or am I better off reworking things to load the reduced psf/PDB files before writing the NAMD configuration files, and using the more straightforward

cispeptide restrain ...
chirality restrain ...

?

On a related note, has anybody ever put together a script to add or remove harmonic restraints to specific atoms in an AutoIMD simulation on the fly? In principle this should be fairly straightforward using TCLForces, but in practice I fear it would take me a long time to do myself.

Thanks,

Tristan

 
 
Tristan Croll
Lecturer
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
 
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