From: Tristan Croll (tristan.croll_at_qut.edu.au)
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.
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On 13 Apr 2015, at 12:37 pm, sunyeping <sunyeping_at_aliyun.com<mailto:sunyeping_at_aliyun.com>> wrote:
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?
Institute of Microbiology, Chinese Academy of Sciences
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