VMD-L Mailing List

From: t.shivam_at_iitg.ernet.in
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
> joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

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.

regards
shivam
>
>
>
>
> 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
>
>
>