VMD-L Mailing List

From: DESPIAU-PUJO Emilie UJF (emilie.despiau-pujo_at_cea.fr)
Date: Tue Jul 17 2012 - 09:58:31 CDT

Dear vmd users,

I use .pdb files containing C and H atoms and I want to represent them as VDW spheres with dynamic bonds (different cutoff distances for C-C, C-H and H-H bonds).
I can manage to render C-C and C-H dynamic bonds but I don't know how to deal with H-H bonds.
Is it because VMD does not include H-H bonds in DynamicBonds drawing method ?
Is there any possibility to circumvent this situation?
Here is what I use in my current .vmdrc file :
# render C and H atoms
color Element C blue
color Element H yellow
display depthcue off
mol modcolor 0 0 Element
mol modstyle 0 0 VDW 0.4 12
mol modselect 0 0 all
# render H-H bonds
mol addrep 0
mol modcolor 1 0 Element
mol modstyle 1 0 DynamicBonds 1.1 0.2 10
mol modselect 1 0 {element H}
# render C-H bonds
mol addrep 0
mol modcolor 2 0 Element
mol modstyle 2 0 DynamicBonds 1.3 0.2 10
mol modselect 2 0 {(element H and within 1.3 of element C) or (element C and within 1.3 of element H)}
mol List
# render C-C bonds
mol addrep 0
mol modcolor 3 0 Element
mol modstyle 3 0 DynamicBonds 1.7 0.2 10
mol modselect 3 0 {element C}
mol List

Could someone help me ?
Many thanks,
Emilie

-------------------------------------------------------------------------------------------
Emilie Despiau-Pujo
LTM / CNRS-UJF-INPG
(CEA/LETI/D2NT)
17 av. des Martyrs, 38054 Grenoble - France
+ 33 (0)4 38 78 48 12