VMD-L Mailing List

From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Fri Aug 21 2020 - 09:03:30 CDT

As far as I know, the psf file is mandatory. Where else will your
simulation program find the masses, charges, and equilibrium values
for your molecules?

On Tue, Aug 18, 2020 at 7:05 AM RAHUL SURESH <drrahulsuresh_at_gmail.com> wrote:
>
> Hi. Thank you for the clarificationa= and I managed to sort that out
>
> 1. Upload the membrane pdb
> 2. 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.pdb
> 7. 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