[gmx-users] Create Bond between new residues

[Richard Broadbent]

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 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists