VMD-L Mailing List

From: Sergey Ivanov (icegood1980_at_gmail.com)
Date: Tue Jul 15 2008 - 10:49:43 CDT

Hello, developers!
I want use VMD program for visualization of rahter beads on mesoscopic
level. In input for VMD i use PDB format with my own meaning of
"molecules" and "bonds". And respectivetly distance units has own
meanings.
I've tested PDB file (see attach) and found out that many bond plugged
to model from "nowhere"... Every "molecule" has not more then 3 bonds
with other ones accordingly to file but i see i quite other picture
and errors through loading:

MolAtom xxx: Exceeded maximum number of bonds (12)

Can you suggest workaround for me? As i understand from log:

            Info) Determining bond structure from distance search ...

- it must be something that determines bond from exactly PDB file and
not "from distance" 

--
Sergey Ivanov