From: Axel Kohlmeyer (
Date: Tue Apr 23 2013 - 04:22:26 CDT

On Tue, Apr 23, 2013 at 10:40 AM, LW <> wrote:
> Dear all,
> As attached, I have a structure of Saposin C in the presence of SDS micelle

there is no attachment.

> solved using NMR. I used a Tcl script to split its 20-structure ensemble
> and took the first model and generated SapC_one_model.pdb. I also have a PDB
> file(as attached )built to model SDS micelle surrounded by water. Does VMD
> allow people to dock these two molecules and generate a combined PDB file
> for further analysis? While the structure of Saposin C in the presence of

VMD doesn't have a "docking software" included, but it can be used to
manipulate/merge structures.

> SDS micelle was solved, NMR data indicate that the open hydrophobic pocket
> is in contact with SDS micelle. Unfortunately, the structure of Saposin C in
> the presence of SDS micelle stands alone, instead of as a complex structure
> in the form of a PDB file. Is it possible to use VMD to determine the
> geometry of the two molecules where (i), they are in intimate contact, (ii),
> there is no clash, (iii), the shape complementarity is at its optimal?

it looks like you should spend some time reading about VMD's
capabilities on the VMD homepage and skim through the user's guide,
tutorials and plugin documentation. if you can find something that
suits your specific needs, then you have what you are asking for.
other than that, you can look elsewhere or consider implementing what
you are looking for through scripting. if anything the most powerful
feature of VMD is that you can *add* functionality (and often far
beyond what the developers originally imagined) through scripting in
either Tcl or python.


> Many thanks in advance.
> Levi

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.