VMD-L Mailing List

From: v.satarifard (v.satarifard_at_ut.ac.ir)
Date: Sun Jul 28 2013 - 03:22:20 CDT

 

Hi dear VMD users:

I generate graphene sheet in vmd with nanotube
builder plugin and I remove some atoms and bonds with Hyperchem and
change position of sheet with translating graphene center of mass t_o
_zero coordinate. After that when I want to merge this manipulated
graphene sheet with special protein (I have pdb and psf file for
graphene and protein) in VMD I faced with error (FATAL ERROR...), also
when I generate graphene with other programs like nanoengineer I faced
with same problem. Is any way to manipulate graphene sheet in VMD
(remove/add some atoms and bonds and translate graphene COM to zero
coordinate)? I need any suggestion/advice for do this work with other
possible way, I just need merge manipulated graphene sheet with special
protein. I use VMD 1.9.2 alpha version.

Thanks

Best,Vahid