[gmx-users] How to connect different parts of a polymer?

Mark Abraham mark.j.abraham at gmail.com
Fri May 22 13:22:46 CEST 2015


Given .rtp entries for the repeat units, pdb2gmx can use the specbond.dat
mechanism to generate cross-links, as it does e.g. for disulfide links in
proteins. See manual.


On Fri, May 22, 2015 at 12:12 PM faride badalkhani <
farideh.khamseh at gmail.com> wrote:

> Dear GMX users
> I am trying to parametrize GROMOS FF for PAMAM dendrimers. I have
> paramerized core of the dendrimer, its repeat units, and terminal groups
> separately. but I dont know how to connect them to build a complete
> dendrimer so that GROMACS can recognize dendrimer structure exactly.
> Could you help me, please?
> Truly yours,
> Farideh
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