VMD-L Mailing List

From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Sat Aug 15 2020 - 17:17:49 CDT

Hi Rahul,

I think we should keep VMD on the thread.

Taking a look at the VMD User Guide will help you fix and understand a
lot of these syntax problems:
https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node122.html
https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node199.html

atomselect molecule_id selection_text [frame frame_number]
Creates a new atom selection and returns its name.

$roll (with two L) is a molecule ID. It contains an integer such as 0, 1, 2,...
$rol (with one L) is an atom selection. It contains a name such as
"atomselect0", "atomselect1", ...
Those names map to atom selections.

The error message has already told you this:

> expected integer but got "atomselect1"Not valid molecule id atomselect1 in atomselect's 'molId'

Your commands to align the POPC to the origin are clearly working.
Aligning a POPC and a nanotube to the origin should be exactly the
same, right? You used one atom selection for the POPC. I don't see why
one atom selection wouldn't work for the nanotube.

You should figure out exactly what the commands and variables stand
for, and exactly why you are using so many of them.

Thanks,
Mortimer

On Sat, Aug 15, 2020 at 8:51 AM RAHUL SURESH <drrahulsuresh_at_gmail.com> wrote:
>
> Hi Hemmit ..
>
> Thank you for the clarification. I still face some problems. SOrry for being a novice.
>
> I have two seperate PDB, membrane construcuted from CHarmm-gui (resname POPC) and NT (resname MOL).
> 1. Upload the membrane pdb
> 2. set popc [atomselect top all]
> 3. set roll [mol new trial.pdb] >>>>>>>>>>>>>>>>>>this load the NT
> 4. set rol [atomselect top "resname MOL"]
> 5. $popc moveby [vecinvert [measure center $popc weight mass]] >>>>now NT is aligned to the center of POPC
> 6. $popc writepdb popc_TEMP.pdb
>
>
> Now i tried
>
> >Main< (Roll_vmd) 17 % set vest [atomselect $rol "resname rol"]
> expected integer but got "atomselect1"Not valid molecule id atomselect1 in atomselect's 'molId'
> >Main< (Roll_vmd) 18 % set vest [atomselect $rol "resname MOL"]
> expected integer but got "atomselect1"Not valid molecule id atomselect1 in atomselect's 'molId'
> >Main< (Roll_vmd) 19 % set vest [atomselect $roll "resname MOL"]
> Cannot find molecule 2 in atomselect's 'molId'
> >Main< (Roll_vmd) 20 % set vest [atomselect resname MOL]
> expected integer but got "resname"Not valid molecule id resname in atomselect's 'molId'
> >Main< (Roll_vmd) 21 % set vest [atomselect $rol "resname resid 1"]
> expected integer but got "atomselect1"Not valid molecule id atomselect1 in atomselect's 'molId'
> rol roll
> >Main< (Roll_vmd) 22 % $rol moveby [vecinvert [measure center $rol weight mass]]
> measure center: molecule was deleted(?)
>
>
> Why could I not do this correctly?
>
> Please help
>
>
> On Fri, 14 Aug 2020 at 06:52, Mortimer Hemmit <mortimer.hemmit_at_gmail.com> wrote:
>>
>> 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
>> > Create your own email signature
>
>
>
> --
> Regards,
> Rahul