[gmx-users] broken protein

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 2 12:54:30 CEST 2009

P.R.Anand Narayanan wrote:
> Dear users,
> How will I be able to run a simulation on a protein with 2chains if it 
> is broken.
> I heard that the protein might have been broken which was observed from 
> the failure of energy minimization which ended in just 1 step.

"Broken" is a very generic term for any sort of bad geometry or 
improperly-manipulated coordinates.  If you can provide a more detailed 
description of your system, what you have done to it (complete with actual 
command lines for any Gromacs tools you have used), etc. you're more likely to 
get a useful response.


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


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