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
Something is really weird about that system.
The error message changes with the number of residues I use.
Everything works fine for 2 and 3 residues. With 4 residues I get :
___
Warning: Starting residue DUL1 in chain not identified as
Hi,
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.
Mark
On Thu, Jun 19, 2014 at 6:11 PM, Soren Wacker
