Date: Thu Nov 30 2017 - 22:10:49 CST

> I’m pretty sure BSA (assuming its bovine serum albumin) is a monomer,
> not a dimer. This means that the second copy in the crystal structure is a
> duplicate relative to the native state, which nicely solves your math
> problem.
> Josh Vermaas
> Director’s Postdoctoral Fellow
> National Renewable Energy Laboratory

yes i also realized it, thanks for confirming my assumption, but is it the
case with all pdb files in the protein data bank, as i experienced the
same with fibrinogen also, do we need to use just half of the fragments
the pfrag command, or the chains given in the file, for creating the psf.

> On Nov 27, 2017, at 1:40 AM,
><> wrote:
> Dear vmd users,
> I am using psfgen for creating psf for BSA protein, so when i am using
> the
> procedure given in the psfgen tutorial (that is creating separate pdbs
> for
> fragments present in the pdb file and building separate segment for each
> segment) i am getting the total charge of -34 on the final structure
> which
> is exactly twice the value reported in the literature (-17) as the
> protein
> had two fragments each has a charge of -17 (i checked it),
> but when i am building the whole protein under single segment (following
> the NAMD basics tutorial) i am getting the correct charge that is -17.
> so which procedure is the correct one or am i making any mistake?
> regards
> shivam