[gmx-users] Topology file for diamond nanocrystal in water

[Гена Ионов]

Hello!

I tried to convert pdb file with small diamond (about 200 atoms of C) into
*.gro and *.top file, but problem in building topology file for 3D net
of bonds in diamond crystall. System not infinite, have water shell
and periodic bonds not appropriate.

Haw I can build such topology file? May be it take into account all 200 atoms?
But then may be exist any software for this automatic generation
topology files for covalent crystal?

Many thanks for any advice.

Gennady V. Ionov.
gionov at mail.ru