[gmx-users] protein fragmented issue for minimization

Justin Lemkul jalemkul at vt.edu
Wed Dec 13 18:53:20 CET 2017

On 12/13/17 12:52 PM, MD wrote:
> Hi Gromacs folks,
> I was trying to minimize a structure of a fragmented protein (part of a
> loop is missing) which makes gromacs keep giving me error messages like bad
> waters, or warnings of nonbonded interactions between particles xxx and
> xxx.
> Is there a solution to let gmx acknowledge the broken structure to start
> with, or I have to manually connect the broken loop in an artificial way?

You have to model the loop in. It doesn't make sense to try to simulate 
a discontinuous protein.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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