From: Raman Preet Singh (
Date: Thu Jun 10 2021 - 05:02:58 CDT

I couldn't really makeout what you intend to do by loading multiple PDBs but you can have a look at MGLTools. MGLTools can load multiple PDBs.


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From: <> on behalf of Pawel Kedzierski <>
Sent: Thursday, June 10, 2021 12:30:01 PM
To: Chris Neale <>; vmd-L <>
Subject: Re: vmd-l: loading multiple different topologies into the same "molecule"

Dear Chris,
This is not really a use case for VMD. The program was designed to
analyze big MD trajectories as efficiently as possible, and that
involved some sacrifices. There is only one copy of topology and
composition data per molecule and it is common to all frames, so the
frames only need storage for frame-specific data, usually just coordinates.

Given the flexibility of the scripting engine, some plugins like
Molefacture do work around some of these limitations, but this approach
in general will not be efficient and there will be always some glitches.
For example, you would need to create a molecule with surplus atoms to
accommodate the largest one in your set, and basically at every change
of the frame you would need to reassign all atom and residue specific
info and recalculate bonds and secondary structures, then update all
your selections and representations. Some things like showing multiple
frames at once will not work/show garbage anyway.

I believe that even if you would write such plugin, it will be painfully
slow to work with, and the work investment will be much larger than
learning another program which does what you want. Sorry for spamming
the VMD list, but I know that Pymol handles frames of different
topologies and it also has selections, multiple representations,
scripting interface (in Python), and is useful for batch generation of
high quality images among other things. However I only tried it with
multi-molecule MOL2 and SDL files with small organic compounds so I do
not know how to load multiple PDB files as frames into Pymol. You may
try to concatenate them and to trick Pymol into thinking that it is a
multi-model PDB like one from NMR.


W dniu 10.06.2021 o 01:34, Chris Neale pisze:
> Dear users:
> does anybody know if it's possible to load many different PDB files
> into the same molecule and have those PDB files have different system
> compositions? An example would be to be able to run "vmd -f *.pdb" on
> a large collection of PDB files of the same protein family, etc. I
> realize that some selection tools would then break (e.g., a selection
> of "resid 19" might not always play nice), but sensible selections,
> like "protein" "water", etc might be OK. I know that there are some
> good ideas with putting particles far away for things like constant pH
> simulations, but that's not as generalizable as loading in all SH2
> domains in the PDB, for example.
> I realize that I could script image generation, or load hundreds of
> separate molecules with a "vmd -m *pdb" command, but none of those is
> as intuitive for browsing structural data where some models may have
> missing residues, insertions, different sequences, different numbers
> of water, etc.
> If such a capability does not exist, can anyone guess how hard it
> would be to implement right in the GUI? I'm not asking for anyone to
> actually do this, just trying to get a sense of how hard it would be.
> PS: I've got 10+ years experience with VMD, and I'm fairly confident
> that this is not possible at the present time. However, I'm asking
> since (a) somebody might have a great alternative solution and (b) in
> any event I'm interested in learning how hard this would be to implement.
> Thank you for your advice,
> Chris.