[gmx-users] additional bond description (isopeptide bond) between two chains

[durdagis]

Hello all,

I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (before pdb2gmx), it looks I need to add additional
description for this bond (between two different chains) at the topology
definition. How can I define it? (please see the picture, this is after
energy min.)

serdar

<http://gromacs.5086.n6.nabble.com/file/n5005445/isopep.png> 



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