QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: ulysse888 on November 29, 2011, 11:52

Title: Ag 111 sheet
Post by: ulysse888 on November 29, 2011, 11:52

Dear Friends and Collegues,

Help me, please. How can I create Ag 111 monolayer sheet, lets say 90x90 angstrem ? this must be exportable to another molecular modeling program as a file with extenson .pdb prferable), xyz,pdbqt,hin, ent etc.
Thank you in advance and sorry for the noob quest,
ulysse :(

Title: Re: Ag 111 sheet
Post by: Anders Blom on November 29, 2011, 12:48

In VNL, take Ag from the Database and move it to the Builder. Then cleave it in the 111 direction, remove two atoms, and repeat in X/Y as needed (40 times or so). You can export as XYZ from the Builder, although you will lose the cell size information since this cannot be encoded into XYZ. An alternative is to export as CIF.

Tip: use OpenBabel (http://openbabel.sourceforge.net/wiki/Main_Page) to convert between different formats (like XYZ to PDB).

Title: Re: Ag 111 sheet
Post by: ulysse888 on November 30, 2011, 14:31

Dear Anders,

Thank yu very much for your replay in forum. I will try to do what you suggest,
thanks again,
Sincerely
Ulysse88


P.S. By the way, I cannot see any picture wiith a code

Title: Re: Ag 111 sheet
Post by: Anders Blom on December 1, 2011, 12:46

I didn't add any picture, so you shouldn't need any code :) Your account is activated, so you will be able to see attachments etc.