VMD-L Mailing List

From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Wed Sep 09 2009 - 09:55:05 CDT

Hello,

I'm new to VMD and am having some difficulties generating
a .psf file for a CNT. I use the plugin extension to
generate the nanotube on the VMD main menu. The generated
tube is then saved w/ the file extension .pdb. Running
autopsf fails which I tracked to the residue named "CNT".
I then renamed all 'CNT' residues to 'CA'. Autopsf then
appears to complete OK, but the VMD command line window
shows a long list of "can't locate coordinates" for each
line from the pdb file (which of course HAS valid
coordinates). The resulting .psf file contains nothing
useful and the autopdb file generated only has a single
atom in it.

Could someone more knowledgeable about VMD please describe
what I'm doing wrong?

Thanks much,

Ron
Research assistant, nanoscience program at UNM