From: Markus Dahlgren (
Date: Mon Jul 29 2013 - 10:02:46 CDT


I have issues figuring out how to first to unwrap a NAMD trajectory and
then wrap waters around it.
My protein ligand complex has three protein chains (A, B, and C) and
three ligands (Chain D, resid 1, 2, and 3).
I can unwrap the system using:
pbc unwrap -first now -all

After I have read an .xsc file, I have attepted many ways to wrap the
waters around the system:
pbc wrap -centersel "chain A to D" -center com -compound residue -first
now -all

Visually the wrapped box looks fine, but when i calculate protein-water
nonbonded energies, using NAMD Energy,
the vdw and coulomb energies will jump from -5000 for some initial
windows to +9.99999e+09 for the remaining windows. Especially
the VdW energies spike, registering +1e+10. This suggests that the
waters are overlapping the protein ligand complex. I get
similar errors if I dont use unwrap before wrap.

I dont know how to get around this problem. If anyone is experienced
with pbc tools and could give me some advice or help, it would be
greatly appreciated. I could supply dcd files, but they are of about 1GB
total size.