VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Feb 03 2015 - 09:21:06 CST

Hi Jevgenij,

Here is how I would do it, assuming you have the latest CHARMM-36
forcefield files from the MacKerell website
(http://mackerell.umaryland.edu/charmm_ff.shtml):

1.) Load the initial pdb into VMD.
2.) rename the certain amino acids you are interested in (ex.
[atomselect top "residue 119"] set resname DALA, which changes residue
119 to D-alanine)
3.) Save a pdb with only the backbone present (backbone.pdb) so that
psfgen will properly assign stereochemistry from the IC tables.
4.) Rebuild the protein with psfgen:

package require psfgen
topology top_all36_prot.rtf
topology toppar_all36_prot_d_aminoacids.str ; #This file will need to
have the parameters taken out of it. Psfgen doesn't ignore the lines it
can't read.
segment P {
pdb backbone.pdb
}
coordpdb P backbone.pdb
guesscoords
writepsf output.psf
writepdb output.pdb

With that, you'll have everything you need for D amino acids.
-Josh Vermaas

On 02/02/2015 08:15 PM, Jevgenij Raskatov wrote:
> Dear users,
>
>
> I would like to introduce chirality inversions (i.e. L- to D- amino
> acid mutation) into a protein. Does anyone have any recommendation on
> how to do it?
>
> So far, I attempted using the following instructions
>
> http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html
>
> However, the resultant non-natural amino acid /DAL/ is not recognized
> by vmd when I load the topology file
>
> I would be very grateful for suggestions
>
> Many thanks in advance
>
> Jevgenij
>
> --
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
>
> Tel.: +1-831-459-2978
>
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA