VMD-L Mailing List

From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Tue Aug 18 2020 - 06:05:04 CDT

Hi. Thank you for the clarificationa= and I managed to sort that out

*1. Upload the membrane pdb2. set popc [atomselect top all]3. set nt [mol
new nt.pdb] 4. set roll [atomselect top "resname ROL"]
  5. $popc moveby [vecinvert [measure center $popc weight mass]] 6. $popc
writepdb popc_TEMP.pdb7. set vest [atomselect $nt "resname ROL"]8. $roll
moveby [vecinvert [measure center $vest weight mass]]9. display resetview *

*10. $roll move [transaxis z -25] 11. $roll writepdb nt_temp.pdb *

Till this everything went well.

As per the tutorial, the next step is to combine both the temp files, which
require psfgen. But here we don't have a psf file for NT.
The command "coordpdb popc TEMP.pdb " ends up with error.

How can I combine both and save as PDB and is PSF mandatory for further
procedures?

Next I skipped this part and started working with bad lipids.
I individually loaded both the temp pdb files.
Followed the tutorial and set beta for popc as 0

*set seltext1 "$POPC and same residue as (name P1 and z>0 and abs(x)<15 and
abs(y)<15)" *
*set seltext2 "$POPC and same residue as (name P1 and z<0 and abs(x)<10 and
abs(y)<10)" *

I did not check how far the above command works.

*set seltext3 "$POPC and same residue as (within 0.6 of protein)" *but
with this command, I am quite confused how to select NT instead of protein.

Expecting your reply. Thank you

On Sun, 16 Aug 2020 at 03:48, Mortimer Hemmit <mortimer.hemmit_at_gmail.com>
wrote:

> 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
> 

-- 
*Regards,*
*Rahul *