[gmx-users] maximum number of specbonds?

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 19 19:06:05 CEST 2014


It sounds like your practical options are to build some larger fragments to
use when required, or generate your topology with something else, e.g. a
custom script. pdb2gmx was built with slightly-branched polymers in mind,
not much else.


On Thu, Jun 19, 2014 at 6:11 PM, Soren Wacker <swacker at ucalgary.ca> wrote:

> Hi,
> I am parameterizing an artifical ligand. I use small residue-like
> fragments and connect them with specbonds in a grid, since I need arbitrary
> shapes and sizes. Now, I ran into segmentation faults, when the grid
> becomes to large.
> Is there an upper limit for the specbonds? How can I fix that or do you
> see a better way to solve that issue?
> Thanks
> Soren
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