atomselect: cannot parse selection text: index (= empty atom selection), lipid residue names not included in membplugin_lipid macro

[Nur Hanna Mardhiyyah]

Hello. I'd like to ask a problem when I try to calculate DLiPS and DLiPC using Lipid Interdigitation.
I have tried using Lipid Interdigitation on my DLPS and DOPS molecule, and it's turned okay. There's no problem. But when I change to DLiPS or DLiPC, it became Error although I use the same step as before. I have loaded .PSF file and .DCD for trajectory, changed the resname so it same as the topology and .PSF or .PDB file.
I've tried to look at another discussion and general requirement but I found nothing. I'm using NAMD and VMD.
Please help me...

Here's the output/log

---

Something went wrong.

Command: interdigitation -structure /home/nurhanna/DinamikaMolekul/DLiPS/DLiPS-third_try/LiS440_ionized_ver2.psf -trajectory /home/nurhanna/DinamikaMolekul/DLiPS/DLiPS-third_try/system-npt-01.dcd -sel {membplugin_lipids and noh} -from 0 -to last -step 1 -zmin min -zmax max -zres 1.0 -zmid auto -cutoff 4.0 -o /home/nurhanna/DinamikaMolekul/DLiPS/DLiPS-third_try/system-npt-01.interdigitation -wrapcmd {pbc wrap -center bb -centersel membplugin_lipid -compound res}

Error:
atomselect: cannot parse selection text: index
atomselect: cannot parse selection text: index
while executing
"atomselect top "index $up_i""
(procedure "::interdigitation::overlap" line 44)
invoked from within
"::interdigitation::overlap -structure /home/nurhanna/DinamikaMolekul/DLiPS/DLiPS-third_try/LiS440_ionized_ver2.psf -trajectory /home/nurhanna/Dinamika..."
("eval" body line 1)
invoked from within
"eval ::interdigitation::overlap $args "
invoked from within
"if $errflag { error "Something went wrong.\n\nCommand: interdigitation $args\n\nError: \n$errMsg" $savedInfo $savedCode }"
(procedure "::interdigitation::interdigitation" line 15)
invoked from within
"::interdigitation::interdigitation -structure /home/nurhanna/DinamikaMolekul/DLiPS/DLiPS-third_try/LiS440_ionized_ver2.psf -trajectory /home/nurhanna/..."
("eval" body line 1)
invoked from within
"eval ::interdigitation::interdigitation $args"
(procedure "interdigitation" line 1)
invoked from within
"interdigitation -structure /home/nurhanna/DinamikaMolekul/DLiPS/DLiPS-third_try/LiS440_ionized_ver2.psf -trajectory /home/nurhanna/DinamikaMolekul/DLi..."
("eval" body line 1)
invoked from within
"eval $cmd"
(procedure "::interdigitationgui::run" line 29)
invoked from within
"::interdigitationgui::run"
invoked from within
".mtinterdigitationgui.run.runbutton invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .mtinterdigitationgui.run.runbutton"
(command bound to event)

[Ismael Rodriguez Espigares]

Dear Nur Hanna Mardhiyyah,

Please check that DLiPS and DLiPC residue names have been added to the configuration file by:

• Clicking on "Configure" button in the Main window (requires writing permissions on VMD installation files inside VMD installation directory or running VMD as root or admin permissions)
• "Use custom lipid resnames" option on the Main window of MEMBPLUGIN.

See [GUIMainwindow].

Best,

Ismael.

EDIT: The second solution for lipid interdigitation does not work. Please, continue reading this thread for the solution that does not require admin or writting permission on VMD installation directory.

[Nur Hanna Mardhiyyah]

Thank you for kindly answer my question.

I use custom lipid resname "DUPS" for my DLiPS, and "DUPC" for my DLiPC. It works well when I try to calculate the DLiPS/DLiPC + cholesterol. But it can't work when I just do the DLiPS/DLiPC only.
(On my DLPS/DOPS only and DLPS/DOPS + cholesterol, it works well)

[Ismael Rodriguez Espigares]

Dear Nur Hanna Mardhiyyah,

I just realized that using "Use custom lipid resnames" does not solve your problem as it is not used by lipid interdigitation, as stated in the wiki.

If you cannot change MEMBPLUGIN configuration file, then "membplugin_lipid" and "membplugin_lipids" will not include DUPS or DUPC residue names ("Use custom lipid resnames" does not change these atom selection macros).

If your system only contains lipids with residue names DUPS, DUPC and CHL1 then you should use the following atom selection in "Selection to analize:" text box of "Lipid interdigitation" window (See [LipidInterdigitation]):

• (resname DUPS DUPC or membplugin_lipid) and noh

Furthermore, you should also change the atom selection in the "Wrap command" box of the Main window (unless you have the "Wrap command" empty because your system is already properly wrapped). If your system only contains lipids with residue names DUPS, DUPC and CHL1 then you should use the following "Wrap command" :

• pbc wrap -center bb -centersel {resname DUPS DUPC or membplugin_lipid} -compound res

See [GUIMainwindow].

Best,
Ismael.

[Nur Hanna Mardhiyyah]

Thank you so much! I've been successfully calculate it. Bless you.