VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Nov 30 2017 - 13:15:38 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
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Nov 27, 2017, at 1:40 AM, t.shivam_at_iitg.ernet.in<mailto:t.shivam_at_iitg.ernet.in> 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