[gmx-users] protein fragmented issue for minimization

MD refmac5 at gmail.com
Wed Dec 13 18:52:16 CET 2017

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

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?

Thank you,


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