[gmx-users] Create Bond between new residues

Richard Broadbent richard.broadbent09 at imperial.ac.uk
Fri May 11 17:38:26 CEST 2012

here is a simple example (for more complex ones see the existing
residues in an aminoacids.rtp)

assume molecule looks like 


where the -'s are bonds

with residues AAA, BBB, CCC containing the corresponding atoms,
then the .rtp should contain something like:

[ AAA ]
[ atoms ]
   A typeA  chargeA 1
[ bonds ]
   A +B

[ BBB ]
[ atoms ]
   B typeB  chargeB 1
[ bonds ]
   B -A
   B +C

[ CCC ]
[ atoms ]
   C typeC  chargeC 1
[ bonds ]
   C -B

the + and - define which direction the connection should go

I hope that's helpful


On Fri, 2012-05-11 at 15:43 +0100, Steven Neumann wrote:
> Dear Gromacs Users,
> I created my own residues in aminoacids.rtp which each is formed of
> one atom. I would like to somehow create bonds between then using
> standart harmonic potential. Could you please advise how to do this?
> Stevem 
> -- 
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