VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 11 2016 - 23:26:40 CDT

Hi,
  I would expect that you could post-process the output of the existing
tool to achieve your desired result with some additional scripting so you
would only accept the candidates that match your particular additional
criteria.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 05, 2016 at 05:25:20PM -0400, Chitrak Gupta wrote:
> Hi everyone,
> Is there a way to find intermolecular salt bridges in VMD? From what I
> understand, the plugin only does intramolecular, i.e. looks for donor and
> acceptor in the same atom selection. Is it possible to look for donors and
> acceptors in different atomselection?
> Specifically, I want to find salt bridges between acidic residues and
> choline N (from POPC lipid) and between basic residues and phosphate
> oxygens (lipid headgroup).
> Regards,
> Chitrak. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
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