Lipid tilt error - Unable to load psf file!

[Sunidhi]

Hello

I have a protein-lipid simulated system. I tried to calculate the lipid
tilt angle between POPI lipids by giving the psf file as structure and xtc
file as trajectory. The following error showed up:

Something went wrong.

Command: lipidtilt -structure
/home/sunidhi/RA/ABCA1/sim1/wholepsf_withoutwater.psf -trajectory
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc -lipid {CHL1
POPI PSM LLPC 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 {{"POPE" "O11 C38"}} -leaf {0 1} -from 0 -to last
-step 1 -sel all -o {/home/sunidhi/RA/ABCA1/sim1/sim1 lipid tilt
POPI.angles} -wrapcmd {pbc wrap -center bb -centersel membplugin_lipid
-compound res}

Error:
Unable to load file '/home/sunidhi/RA/ABCA1/sim1/wholepsf_withoutwater.psf'
using file type 'psf'.
Unable to load file '/home/sunidhi/RA/ABCA1/sim1/wholepsf_withoutwater.psf'
using file type 'psf'.
while executing
"mol new $psffile"
(procedure "::lipidtilt::tilt" line 45)
invoked from within
"::lipidtilt::tilt -structure
/home/sunidhi/RA/ABCA1/sim1/wholepsf_withoutwater.psf -trajectory
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1..."
("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/wholepsf_withoutwater.psf -trajectory
/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottran..."
("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/wholepsf_withoutwater.psf} -trajectory
{/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.x..."
("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 inform what went wrong. Thanks in advance.

---

Sunidhi

[Ismael Rodriguez Espigares]

Dear Sunidhi,
It seems that your PSF file is not valid. Try to generate a valid PSF file and to open it with VMD using the File > New molecule window before running computations with MEMBPLUGIN.

The only thing we can offer you is link to a Research Gate question that gives several strategies to produce a PSF file from GROMACS files https://www.researchgate.net/post/how_to_generate_PSF_from_GROMACS_PDB

Also, we are do not provide support for how to use the top2psf.pl file, but we know that some version of that file (if not all) require that all topololy data is presented in a single file as it does not parse references to to other files (e.g .itp files).

I am sorry that we cannot help you further with the generation of PSF file, althought it is a common problem among GROMACS community VMD users.

Best,
Ismael.