Re: Can NAMD simulation solve the problem of coordinate clash in a structural model?

From: Tristan Croll (
Date: Fri Apr 17 2015 - 16:50:07 CDT

In general, no. First, you need to inspect the clashes to evaluate their source and seriousness. What is the source of your complex: an experimental structure or docking? Both can have substantial (but different types of) errors.

In either case, rather than starting a simulation from your clashing coordinates and hoping for the best, why not try the following? First separate the offending interface by a rigid-body translation of one protein away from the interface. Then, with careful restraints applied (secondary structure, chirality and cispeptide as a minimum), run an implicit solvent simulation in which you bias the backbone atoms back towards their original positions. This gives everything at the interface a better chance to settle into a favorable arrangement.

Tristan Croll
Faculty of Health
School of Biomedical Sciences
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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On 13 Apr 2015, at 12:37 pm, sunyeping <<>> wrote:

Dear all,

I modelled a structural model of a complex containing two large proteins. There are serious coordinate clashes between these two proteins in the model. Can I expect to do NAMD simulation to solve the problem of cooridnate and obtain a more rational model?

Best regards,

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

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