Fwd: Re: [gmx-users] restraints on water oxygen atoms

Justin Lemkul jalemkul at vt.edu
Tue Jun 11 15:49:46 CEST 2013

I was having issues with my email earlier today, so some things did not go 
through.  Apologies if this is a multiple post, but I wanted to make sure it got 
through, especially since it provides resolution to a very long-running thread:

On 6/11/13 7:46 AM, Shima Arasteh wrote:
> I put the output file of shrinking steps after 32 iterations:
> https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN

I see it now.  Your protein is very small.  InflateGRO works by deleting lipids
based on the distance between C-alpha and P atoms.  Your protein isn't even in
the plane of the P atoms (as most proteins are) and thus very few are likely
deleted.  There is probably atomic overlap in the first (inflated) structure.

Increase the deletion radius in the inflation step, and inspect very carefully
using the visualization software of choice.  If the initial (inflated) structure
is devoid of clashes, so too should any structures in the shrinking steps.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list