[gmx-users] protein fragmented issue for minimization

[MD]

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?

Thank you,

Ming