QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: sweta on February 27, 2012, 07:33

Title: how to make pantacene geometry
Post by: sweta on February 27, 2012, 07:33

Hi everyone,

Can anyone please tell me how to make pentacene geometry in ATK builder?????

Thanks in Advance!

Title: Re: how to make pantacene geometry
Post by: Anders Blom on February 27, 2012, 17:05

How about this:
1. Google "pentacene pdb"
2. Go to first link (http://www.t3db.org/toxins/T3D0629)
3. Open the PDB file (you could take the MOL file too, but it has coordinates in Bohr, I think), PDB is in Angstrom, making it a bit easier
4. Copy the HETATM part, paste in your favorite editor and convert to XYZ format (I use Excel, it has a wonderful "text to columns" function)
5. Save as XYZ file (see attachment)
6. Bring into VNL

You could build it in VNL too, in particular in the new Builder coming in 12.2, but it will still take longer time than the steps above ;)