[gmx-users] defining parameters in a separate itp file

[Dave M]

Hi All,

I am trying to define a bond between two molecules. Their parameters are
defined in separate itp files: molA.itp and molB.itp. I know I can
combine both the itp files but I am just wondering if I can define extra
bonds/angles joining two molecules in a separate itp file taking care of
atom numbers. To test it I defined an extra bond joining two atoms (elastic
bond) from two molecules in a separate bond.itp file but it does not look
like molecules come close at all.
Not sure this is a correct way. And, also is there a way I can print the
bond parameters from tpr file to confirm whether all the bonds and angles
are read from itp files.

My top file looks like this

#include "mol1.itp"

#include "mol2.itp"

#include "bond.itp"


[ system ]

test


[ molecules ]

; name        number

molA 1

molB 1


Thanks.
Dave