VMD-L Mailing List

From: Craig Maloney (cmaloney_at_kitp.ucsb.edu)
Date: Tue Nov 08 2005 - 20:01:52 CST

Hi all.

I have a single monolithic pdb file which has what is essentially an
entire MD trajectory in a single file. There are CONECT records
which I understand are not honored by VMD.

Before I spend time figuring out / installing psfgen and/or x-plor, I
was wondering if someone could recommend one over the other for this
simple job. Will psfgen (as distributed with VMD) write a correct
psf file with bond info given the CONECT record in my monolithic pdb
file, or will it require some manual intervention? Bonds DO break
dynamically, mind you. I don't know if this is an abuse on my part
of the pdb spec or not. If some manual futzing would be required, I
would much prefer to do my futzing with x-plor in python as I'm a tcl
novice.

It's very convenient for me to have my trajectory sit in a single pdb
file, and VMD understands what I want it to do beautifully now, but
will the approach of a single monolithic pdb file (along with a
corresponding single monolithic psf file) still work when I add bonds?

Anyway, any thoughts would be appreciated.

Thanks,
Craig