[ase-users] help

[Niels Bendtsen Halck]

Hi 

ASE is not fantastic at creating molecules of a certain size. 

If you have all the atomic positions relative to each other you can build the molecule as the N2 molecule in the tutorial here

https://wiki.fysik.dtu.dk/ase/tutorials/atomization.html

I have found a PDB 

This is very time consuming. 

I would suggest that you construct a graphene sheet to create the skeleton and then modify the atoms needed using the ASE-GUI tool. The ASE-GUI offer moving and manipulation of atoms with a visual interface.

Sincerely
Niels Bendtsen Halck
Postdoc
DTU Energy
Bygning 309
2800 Kgs. Lyngby
ntben at dtu.dk
________________________________________
Fra: ase-users-bounces at listserv.fysik.dtu.dk [ase-users-bounces at listserv.fysik.dtu.dk] på vegne af Franck Olivier Ngassam Nyakam via ase-users [ase-users at listserv.fysik.dtu.dk]
Sendt: 8. marts 2017 09:48
Til: ase-users at listserv.fysik.dtu.dk
Emne: [ase-users] help

Hello sir I would like to deposit the molecule of (MnPc phthalocyanine) on Ag (111) and I do not know how to build this molecule on ASE. Can you help me please?