Errors stopping SCD calculation

[Albert]

Dear,

I've simulated a membrane system with mixed lipids including:
POPC,POPE,POPS and CHL1. I would like to calculate the lipid order for
each of them. However, when I try to run the VMD plugin, it always
failed with the following information. I am just wondering how to fix it?

thanks a lot

---

Command: membranescd -structure memb.gro -trajectory memb.xtc -lipid
{CHL1 SM18 DLPA DLPC DLPE DLPG DLPS DMPA DMPC DMPE DMPG
    DMPS DPPA DPPC DPPE DPPG DPPS DSPA DSPC DSPE DSPG DSPS POPA POPC
    POPE POPG POPS SOPA SOPC SOPE SOPS SOPG DOPA DOPC DOPE DOPG DOPS
    SAPA SAPC SAPE SAPG SAPS SDPA SDPC SDPE SDPG SDPS DAPA DAPC DAPE
    DAPG DAPS DXPC DXPE DXPS PLPC PLPE PLPS SLPC SLPE SLPS DGPC DGPE
    DGPS DEPC DEPE DEPS DNPC DNPE DNPS PMPE PMPG QMPE OSPE PSPG IPPC
    APPC PHPC} -leaf {0 1} -chain {2 3} -from 0 -to last -step 1 -sel
{not resname CHL1} -o ./order/memb.orderparSCD -wrapcmd {pbc wrap
-center bb -centersel membplugin_lipid -compound res}

Error:
can't read "ntopo": no such variable
can't read "ntopo": no such variable
    while executing
"return $ntopo"
    (procedure "fixupChainNumbers" line 23)
    invoked from within
"fixupChainNumbers $ttopo"
    (procedure
"::membranetool_common::topology::setOccupancyBetaFromTopolog..." line 39)
    invoked from within
"::membranetool_common::topology::setOccupancyBetaFromTopology
"$atomselection and resname $lipids" 10"
    (procedure "::membranescd::orderPar" line 27)
    invoked from within
"::membranescd::orderPar"
    (procedure "::membranescd::scd" line 88)
    invoked from within
"::membranescd::scd -structurememb.gro -trajectory memb.xtc"
    ("eval" body line 1)
    invoked from within
"eval ::membranescd::scd $args"
    invoked from within
"if $errflag {
    catch { set ::membranescd::progress_text {}}
    error "Something went wrong.\n\nCommand: membranescd
$args\n\nError: \n$errMsg" $sa..."
    (procedure "::membranescd::membranescd" line 17)
    invoked from within
"::membranescd::membranescd -structure memb.gro -trajectory memb.xtc"
    ("eval" body line 1)
    invoked from within
"eval ::membranescd::membranescd $args"
    (procedure "membranescd" line 1)
    invoked from within
"membranescd -structure {memb.gro} -trajectory {memb.xtc"
    ("eval" body line 1)
    invoked from within
"eval membranescd $command_line"
    invoked from within
"if $errflag {
    error $errMsg $savedInfo $savedCode
  }"
    (procedure "::membranescdgui::scd" line 121)
    invoked from within
"::membranescdgui::scd"
    invoked from within
".mtscdgui.buttons.runbutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .mtscdgui.buttons.runbutton"
    (command bound to event)

[Ismael Rodriguez Espigares]

Dear Albert,

It seems you have not supplied an structure file with topology information to membplugin. I would recommend that you visualise in VMD the GRO file to check if VMD display bonds correctly. In any case is highly recommended to provide a PSF file to membplugin to retreve topological information.

Please see [GeneralRequirements] .

Best,
Ismael.

[Albert]

thanks a lot for your quick reply.

Initially I supplied .pdb and .xtc files for the calculation. Now I used
.gro and .xtc files, it seems to work finally.

thanks a lot

On 02/04/2020 05:57 PM, Ismael Rodriguez Espigares wrote:

Dear Albert,

It seems you have not supplied an structure file with topology
information to membplugin. I would recommend that you visualise in VMD
the GRO file to check if VMD display bonds correctly. In any case is
highly recommended to provide a PSF file to membplugin to retreve
topological information.

Please see [GeneralRequirements]
https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/ .

Best,
Ismael.

---

problem of SCD calculation
https://sourceforge.net/p/membplugin/discussion/general/thread/e3fe4aa493/?limit=25#1550/689d

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[Albert]

Hello,

I have finished SCD calculation for a POPC/POPE miexed lipids sytem. I
calculated the SCD separated in the "membrane SCD" gui.

when the jobs were done, I clicked "plot". What surprised  me is that
the plots for POPC and POPE in VMD were exactly the same. However, when
I open the "popc.orderparSCD" and "pope.orderparSCD" files, the values
were totally different.

I don't know why. I am just wondering how shall we plot the
"popc.orderparSCD" file correctly? I noticed that the figure 3 in
"CaseStudy_v1.pdf" tutorial file looks very nice as indicated below:

If possible, would you please share your scripts?

thanks a lot

Albert

[Ramon Guixà-González]

Hi Albert,

I could not find the exact one I used, but please find attached this zip file containing a folder where I used a preliminary version of the script I used to plot order parameters in the case study. If you are a little familiar with R, this should be useful.

Best,
Ramon

[Sunidhi]

I tried using MEMBPLUGIN for the first time but I am not getting any plot due to the stated error:
can't read "data_d": no such variable
can't read "data_d": no such variable
while executing
"dict for {X X_l} $data_d {

    lappend Xlist $X
    lappend Ylist [lindex $X_l 0]
    lappend Errlist [lindex $X_l 1]


}"
("default" arm line 11)
invoked from within

"switch -- $dataswitch {

area {
  set stdflag 0
  set stderrflag 0
  set residues_num [lsearch -nocase -glob -inline $headers {..."
(procedure "::membranetool_common_gui::plotXYErr" line 44)
invoked from within

"::membranetool_common_gui::plotXYErr Carbon -SCD STD_Error "${::membranescdgui::outputfile}_plot~" "Membrane SCD" {Carbon no.} -SCD {Standard error} ..."
invoked from within
".mtscdgui.buttons.plotbutton invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .mtscdgui.buttons.plotbutton"
(command bound to event)

I loaded a .gro file and a .xtc file and clicked "Run". It was done successfully as the message "Done" was reflected. However, when I clicked "Plot", the above stated error is shown. Kindly help.

[Ismael Rodriguez Espigares]

Could please check if output files are not empty?
It could be a matter of atom selections or that your lipid resnames are not in the default list and you'll need to setup a custom residue name list in the main membplugin window.

[Sunidhi]

Yes they are.

On Sun, 26 Apr 2020, 12:57 Ismael Rodriguez Espigares, ismresp@users.sourceforge.net wrote:

Could please check if output files are not empty?

Errors stopping SCD calculation
https://sourceforge.net/p/membplugin/discussion/general/thread/e3fe4aa493/?limit=25#6a29/28fa

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[Ismael Rodriguez Espigares]

The default list of lipid resnames are the ones included the CHARMM-GUI (CHARMM36 force-filed). Are you using custom resnames or a different force-field from CHARMM?

[Sunidhi]

Hey Ismael,

As suggested by you, I converted my individual ITP file of the lipid to the
PSF format using the perl script (top2psf.pl) but the following errors were
thrown on terminal:

vmd > Lipidtilt) Executing: lipidtilt -structure
{/home/sunidhi/RA/ABCA1/sim1/POPC_conv.psf} -trajectory
{/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc} -lipid
{CHL1 SM18 DLPA DLPC DLPE DLPG DLPS DMPA DMPC DMPE DMPG
DMPS DPPA DPPC DPPE DPPG DPPS DSPA DSPC DSPE DSPG DSPS POPA POPC
POPE POPG POPS SOPA SOPC SOPE SOPS SOPG DOPA DOPC DOPE DOPG DOPS
SAPA SAPC SAPE SAPG SAPS SDPA SDPC SDPE SDPG SDPS DAPA DAPC DAPE
DAPG DAPS DXPC DXPE DXPS PLPC PLPE PLPS SLPC SLPE SLPS DGPC DGPE
DGPS DEPC DEPE DEPS DNPC DNPE DNPS PMPE PMPG QMPE OSPE PSPG IPPC
APPC PHPC} -diatom {{"POPC" "O11 C38"}} -leaf {0 1} -from {0} -to
{last} -step {1} -sel {all} -o {/home/sunidhi/RA/ABCA1/sim1/sim1 lipid tilt
angle POPC after psf.angles} -wrapcmd {pbc wrap -center bb -centersel
membplugin_lipid -compound res}
Info) Using plugin psf for structure file
/home/sunidhi/RA/ABCA1/sim1/POPC_conv.psf
psfplugin) WARNING: no angles defined in PSF file.
psfplugin) WARNING: no dihedrals defined in PSF file.
psfplugin) WARNING: no impropers defined in PSF file.
psfplugin) no cross-terms defined in PSF file.
Info) Analyzing structure ...
Info) Atoms: 134
Info) Bonds: 133
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0
lipidtilt) Running Lipid tilt angle...
ERROR) BaseMolecule: attempt to init atoms while structure building in
progress!
ERROR) Invalid number of atoms in file: 132423
Info) Using plugin xtc for coordinates from file
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc
ERROR) Incorrect number of atoms (132423) in
ERROR) coordinate file
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc
ERROR) Mismatch between existing molecule or structure file atom count and
coordinate or trajectory file atom count.
Info) Finished with coordinate file
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc.

Kindly help.

[Ismael Rodriguez Espigares]

Could post also the command that is printed in the terminal/cmd/tcl/tk console of VMD?

[Sunidhi]

I am using a resname which is not present in the resname list. I have that
lipid resname in my files but it's not included in the list and the
following error is thrown:

Something went wrong.

Command: lipidtilt -structure /home/sunidhi/RA/ABCA1/sim1/POPI_conv.psf
-trajectory /home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc
-lipid {CHL1 SM18 DLPA DLPC DLPE DLPG DLPS DMPA DMPC DMPE DMPG
DMPS DPPA DPPC DPPE DPPG DPPS DSPA DSPC DSPE DSPG DSPS POPA POPC
POPE POPG POPS SOPA SOPC SOPE SOPS SOPG DOPA DOPC DOPE DOPG DOPS
SAPA SAPC SAPE SAPG SAPS SDPA SDPC SDPE SDPG SDPS DAPA DAPC DAPE
DAPG DAPS DXPC DXPE DXPS PLPC PLPE PLPS SLPC SLPE SLPS DGPC DGPE
DGPS DEPC DEPE DEPS DNPC DNPE DNPS PMPE PMPG QMPE OSPE PSPG IPPC
APPC PHPC} -diatom {{"POPI" "O11 C38"}} -leaf {0 1} -from 0 -to last
-step 1 -sel all -o /home/sunidhi/RA/ABCA1/sim1/POPI.angles -wrapcmd {pbc
wrap -center bb -centersel membplugin_lipid -compound res}

Error:
No lipids within lipid selection.
No lipids within lipid selection.
while executing
"error "No lipids within lipid selection.""
(procedure "::lipidtilt::tilt" line 66)
invoked from within
"::lipidtilt::tilt -structure /home/sunidhi/RA/ABCA1/sim1/POPI_conv.psf
-trajectory /home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc
-lip..."
("eval" body line 1)
invoked from within
"eval ::lipidtilt::tilt $args "
invoked from within
"if $errflag { error "Something went wrong.\n\nCommand: lipidtilt
$args\n\nError: \n$errMsg" $savedInfo $savedCode }"
(procedure "::lipidtilt::lipidtilt" line 18)
invoked from within
"::lipidtilt::lipidtilt -structure
/home/sunidhi/RA/ABCA1/sim1/POPI_conv.psf -trajectory
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc..."
("eval" body line 1)
invoked from within
"eval ::lipidtilt::lipidtilt $args"
(procedure "lipidtilt" line 1)
invoked from within
"lipidtilt -structure {/home/sunidhi/RA/ABCA1/sim1/POPI_conv.psf}
-trajectory
{/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc} -lipid
{..."
("eval" body line 1)
invoked from within
"eval lipidtilt $command_line"
(procedure "::lipidtiltgui::tilt" line 85)
invoked from within
"::lipidtiltgui::tilt"
invoked from within
".mttiltgui.run.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .mttiltgui.run.button"
(command bound to event)

KIndly help.

[Ismael Rodriguez Espigares]

Dear Sunidhi,
It seems that you have non-standard CHARMM resnames in your simulation (especialy the "POPI" one).
Please, before opening any MEMBPLUGIN computation tool please write in the "Main window" "Lipid resnames:" field all the residue names for the lipids that you have in your simulation separated by spaces after marking the " Use custom lipid resnames:" checkbox.
[GUIMainwindow]
Alternatively, you may add any missing residue names to the "lipids" variable in the MEMBPLUGIN configuration file that you can edit by on the "Configure" tool in the "Main window" of MEMBPLUGIN. These way your changes will be persistent.
Keep in mind that the custom lipids in the main "Main window" overrides the "lipids variable in the config file".
You may need need writting permission to the configuration file in the MEMBPLUGIN installation path.
You can obtain the path to the configuration file by running the following command in VMD main window > Extensions > TK Console:

puts $env(MEMBPLUGIN_DIR)/config.tcl

Just keep in mind that those residue names must correspond ONLY to membrane lipids.

Best,
Ismael.