From: Francesco Pietra (
Date: Mon Jun 03 2013 - 09:42:28 CDT

How to show bonds created with the"bond" command of LEaP?

For example bond PROT.166.CA PROT.365.C15

where, 166 is a standard aa, while 365 is a metal cluster ab initio
parameterized. The two atoms are at bonding distance, but not shown in the
graphical representation.

I am familiar with psf/pdf, while I don't know how to verify from
prmtop/crd the formation of bonds. At any event, I would like to represent
also the extra the bonds created with LEaP on the VMD image.


francesco pietra