VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jan 24 2012 - 13:35:22 CST

Hi,

If you allready have the topology files for your spin label you can use
psfgen to attach the spin label to the protein.
(I'm using MTSL as a spin label -- the parameter files are from this
article<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766176/?tool=pubmed#SD1>).
Attached is an example script

Good luck,
Ajasja
_________

#the resid of the position to mutate to the spin label
set mutpos 18
set pdbname example.pdb
set outname example-out

package require psfgen
resetpsf
#load the topology files (please adjust the paths and names#
topology ../FF/top_all22_prot.rtf
topology ../FF/top_all36_lipid.rtf
topology ../FF/top_all27_R1A.rtf

segment P {
  first NTER
  last CTER

  pdb $pdbname
  mutate [string trimleft $mutpos 0] R1A
}

coordpdb $pdbname P

guesscoord

#mutation-notmin
writepsf $outname.psf
writepdb $outname.pdb

On Mon, Jan 23, 2012 at 21:55, Anna Kuznetsova <kuznetsova.ann_at_gmail.com>wrote:

> Hello dear VMD users!
>
> I am a bit new to vmd although I am using it to visualize and rotate my
> calculated protein structures.
>
> I have a peptide pdb and I need to modify its cysteines with spinlabel IAP
> to create picture that shows peptide with spinlabels attached to its
> cysteines.
>
> Could you please send me script how to attach spinlabels to peptide... or
> an example of PDB with spinlabels already added?
> Or if you could advise me on how to make and attach IAP spinlabel to
> protein in vmd... or if you could advise how to attach any atom to protein
> structure I could build it myself.
>
> Any help would be much appreciated!
>
> Thank you very much for all your help you have given me so far
>
>
> --
> Best regards,
> Anna Kuznetsova
> Joanna R. Long research group
> University of Florida
>