VMD-L Mailing List

From: Rogan Carr (rogan_at_ks.uiuc.edu)
Date: Tue Feb 16 2010 - 09:24:06 CST

Hi Biplab,

If you want to change all HIS to HSD or HSE, you can use a pdbalias
command. If you want to have different residues do different things,
you just have to change them "by hand" in VMD, with TCL commands like

set hse [atomselect $my_molecule "residue XXX"] ;# where XXX is your
residue of interest

$hse set resname HSE

Do the same thing for HSD, save the file as a new PDB ($hse writepdb
"my_new_pdb.pdb"), and load this PDB through psfgen.

If you're new to the scripting interface, there are various tutorials
on how to use it online: http://www.ks.uiuc.edu/Training/Tutorials/ .

Rogan

On Feb 15, 2010, at 11:10 PM, BIPLAB NANDI wrote:

> Hi All,
>
> I am new in VMD.I want to create a PSF file of my protein which have
> two histidine residue.Now I want to assign one histidine as HSP
> state keeping other as HSD state in the psf file. How can I do these
> through autopsf plug-in? Please help me.
>
> Thanks in advance.
>
> BIPLAB