towhee-users Mailing List for MCCCS Towhee

Dear Friends,

Recently I am learning Towhee and have some questions:

1) I have PDB file of a molecule. Can I use pdb file directly or need I
convert pdb to towhee_coords file? And how to convert?

2) For invib, do I need to list all atoms following the pdb file? Or I only
list different types of atoms?

3) For ijvib, I did not figure out the meaning of each number?

4) In the examples, I saw 'd0' in some items, like 'kalp 5.6d0'. I thought
the unit is Angstrom.

5) How to consider a system containing different molecules?

6) Finally, in my system, there is no solvent. What value should be for
'dielect'?


Thank you so much in advance!

Jane

Case Western Reserve University
2104 Adelbert RD, Bingham Building 203C
Cleveland, OH 44106
E-mail: jx...@ca...