VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Dec 28 2008 - 08:55:03 CST

Have you tried just simulating it to see what happens? Four residues
is only one turn of a helix and probably won't maintain that
structure unless it's part of a larger helix. Even if it is, unless
the energy barrier between the two conformations is high, it's quite
likely that it will adopt the structure you expect in the simulation.

NAMD in general knows nothing of secondary structure (this is not
quite true in the latest version though); therefore, trying to embed
secondary structure using HELIX flags in a pdb will not work, and
should not even. If the conformational changes don't occur naturally
in the simulation, your best bet is probably using AutoIMD or even
just moving certain residues in VMD to approximate what you want
(minimization can fix any extended bonds you make).

On Dec 28, 2008, at 1:18 AM, MIke S wrote:

> 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)
>
>
>
>
>