[gmx-users] How to define cross-linking bonds

Jon Mujika joni.mujika at ehu.es
Tue Mar 14 15:32:08 CET 2017

Dear Gromacs users,

I am preparing a system made of polymer chains, which are cross-linked,
that is, there are covalent bonds between residues of different chains. I
have managed to built the structure, including the linking. To do that, I
used the specbond.dat file, where I specified the geometrical criteria to
consider a link covalent bond, replacing the corresponding residues by new
ones (with the C atoms involved in the covalent bond deprotonated). This is
analogous to define disulphur bridges in a protein.

Once the new covalent bonds are identified and the protonation state of the
C atoms updated, I guess I need to assign the bond parameters (force
constant and r0 value) for these new linking bonds. How should I proceed to
add these parameters to the topology file? I would really appreciate any
help in this issue.

Many thanks in advance

Jon Mujika

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