From: LW (wli148_at_aucklanduni.ac.nz)
Date: Tue Apr 23 2013 - 03:40:47 CDT

Dear all,
As attached, I have a structure of Saposin C in the presence of SDS micelle
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 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?
Many thanks in advance.
Levi