VMD-L Mailing List

From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Thu Aug 13 2020 - 20:21:55 CDT

There is a slight syntax error in your script. Look at the moveby
commands after variable substitution.

$popc moveby...
$roll moveby...

$popc is an atom selection, while $roll is a molecule ID, That is why
it complains that a number is an invalid command name.

moveby should be preceded by an atom selection. You should figure out
which variable contains the atom selection for the tube.

Mortimer

On Thu, Aug 13, 2020 at 7:47 AM RAHUL SURESH <drrahulsuresh_at_gmail.com> wrote:
>
> Hi.
>
> I am trying to simulate organic nanotube in lipid bilayer. At this place as the nanotube is having 650 atoms, I couldn't find a way to generate PSF files.
>
> I have two files roll.pdb and membrane.pdb. (Both the pdb files don't have chain id)
>
> My commands are
>
> >Main< (Roll_vmd) 12 % set popc [atomselect top all]
> atomselect0
>
> >Main< (Roll_vmd) 14 % set roll [mol new trial.pdb]
> 1
>
> >Main< (Roll_vmd) 17 % $popc moveby [vecinvert [measure center $popc weight mass]]
> >Main< (Roll_vmd) 18 % $popc writepdb popc_temp.pdb
>
> BY this step, I have the pdb file for popc and water molecules with chain ID X for all the molecules (popc and water)
>
> >Main< (Roll_vmd) 19 % set vest [atomselect $roll "resname MOL"]
> atomselect1
> >> How do I know what atoms are selected in this "atomselect1"
>
> >Main< (Roll_vmd) 21 % $roll moveby [vecinvert [measure center $vest weight mass]]
> invalid command name "2"
>
> I have tried various options and still I couldn't find the way to align the roll to the center of the lipid and remove the bad lipids.
>
>
>
>
>
> --
> Regards,
> Rahul
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