[gmx-users] Create Bond between new residues

[Steven Neumann]

Well, impressive explanation! Thank you very much!

Steven

On Fri, May 11, 2012 at 4:38 PM, Richard Broadbent <
richard.broadbent09 at imperial.ac.uk> wrote:

> here is a simple example (for more complex ones see the existing
> residues in an aminoacids.rtp)
>
> assume molecule looks like
>
> A-B-C
>
> 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
>
> Richard
>
> 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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