VMD-L Mailing List

From: MIke S (vmd.namd_at_gmail.com)
Date: Sun Dec 28 2008 - 01:18:23 CST

Hello,

I would like to modify the secondary structure of my protein prior to
running a simulation in NAMD.

Currently when I load the (crystallographic) PDB in VMD certain residues
(78-81) are helical. However, I would like to change these residues to be
turns or coils since NMR data show that these residues are not in
fact helical (ie. the conditions used in the crystallographic study promoted
helical formation in this region of the protein).

I've glanced at some of the previous messages posted on VMD with regards to
STRIDE and making changes to secondary structure. I've tried the suggestion
in this post
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/0849.html which
worked, however when I tried to save the corresponding PDB file the changes
to the secondary structure weren't preserved. Obviously, using the
'structure' command only changes the graphic image of the protein in the VMD
display...and my knowledge of STRIDE is slim. I was hoping to save a PDB
file with the corresponding structural changes and follow that up with a run
of psfgen to generate the necessary PSF and PDB files for my NAMD
simulations.

How can I make the necessary changes to the protein structure and save this
to a file? I assume I will need to manipulate some of the data listed in
the PDB or PSF files. In fact, I've played around with the HELIX string in
the PDB file and modifyed the residues listed in the HELIX string of
interest, but it didn't work - at least when I checked the structure on VMD
the residues were still helical. Also, if I need to manipulate the
dihedral angles for example, how do I know which phi and psi values to use
for a coil or turn?

Some side notes:

There aren't any NMR PDB files of the full protein that I'm aware of. In
addition to the above residues there are other residues that would need
structural changes. I've used the program SwissPDB Viewer to add missing
residues (1-4) and for some reason these residues are helical even though
they should be coiled. (For those familiar with SwissPDB: I've tried to
change the secondary structure using the control panel in SwissPDB
before importing to VMD, but the structure remains helical). Btw, I'm using
the latest versions of VMD and NAMD.

I hope someone can offer some assistance.

Happy Holidays,

Mike

(PS. I also posted this on the NAMD mailing list)