From: Peter Freddolino (
Date: Tue May 29 2007 - 12:16:16 CDT

Hi Mark,
right now the mol2 plugin is only designed to read a single frame,
because as far as I could tell from Tripos's mol2 standard, that's all
the file format is supposed to have. If you could send me an example
file and (preferably) some sort of documentation for how people usually
lay out multi-frame mol2 files, we can try to support this (as long as
there's a consensus for what they whould look like). In the meantime, it
should be fine if you convert your trajectory into some other format
that supports multiple frame input (you can still load a mol2 file to
establish the topology, and then add a trajectory file to it).

Mark Zottola wrote:
> I have a trajectory from an MD run stored as a MOL2 file. I can read
> inthe mol2 file but VMD only sees one frame. If I read in a MOL2 file
> having only the initial frame of the MD run then try to "load data
> into molecule" by reading in the MOL2 file containing the entire
> trajectory, VMD thinks there are only 2 frames to the simulation.
> Would this problem be circumvented if I could convert the MOL2 file to
> an SD file?
> Thanks for any pointers you can give.
> Mark