VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Wed Mar 05 2014 - 11:30:29 CST

Right after you load your molecule into VMD, do the following:

set sel [atomselect top "selection_to_delete"]
set atomList [lsort -unique [$sel get {segname resid}]]
$sel delete

package require psfgen
resetpsf

readpsf original_psf_file.psf
coordpdb original_pdb_file.pdb

foreach atom $atomList {
        delatom [lindex $atom 0] [lindex $atom 1]
}

writepsf output.psf
writepdb output.pdb

--------------

You can also try the following:

set sel [atomselect top "not (selection_to_delete)"]
$sel writepsf output2.psf
$sel writepdb output2.pdb
$sel delete

But check if the second approach gives you the same result as the first one.

-Maxim

On Mar 5, 2014, at 11:09 AM, Pavan Miriyala <pavan.kumar9111_at_gmail.com> wrote:

> My atom name is like this GRA 198:C, it's molecular i.d is 2, name C, residue 0, resname GRA, resid 113
> Now I have to select the atom and delete it using atomselect please help me.
>
> Thanks & Regards,
> Venkata Pavan Kumar. Miriyala
> pavan.kumar9111_at_gmail.com,
> contact number: +91-9032307746
>
>
>
> On Wed, Mar 5, 2014 at 10:31 PM, Pavan Miriyala <pavan.kumar9111_at_gmail.com> wrote:
> I'm very new to vmd. Could you please tell me how to delete atoms through vmd tcl console atom select command?
>
> Thanks & Regards,
> Venkata Pavan Kumar. Miriyala
> pavan.kumar9111_at_gmail.com,
> contact number: +91-9032307746
>
>
>
> On Wed, Mar 5, 2014 at 10:23 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> Hi there,
>
> Take a look at psfgen and its “delatom” command.
>
> psfgen user's guide is here:
> https://www-s.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf
>
> Maxim
>
>
> On Mar 5, 2014, at 10:21 AM, Pavan Miriyala <pavan.kumar9111_at_gmail.com> wrote:
>
> > Hello sir,
> > I made a single layer graphene sheet using nano-builder plug-in. Now I wanted to form a crack in that sheet, for that I'm thinking to delete atoms and bonds in that particular sheet. Please help to do that
> >
> > Thanks & Regards,
> > Venkata Pavan Kumar. Miriyala
> > pavan.kumar9111_at_gmail.com,
> > contact number: +91-9032307746
> >
>
>
>