I have a system with a protein and a lipid membrane together. The membrane has 7 different lipid types but only POPC throws the following error while running MEMBPLUGIN:
Error:
vecdot needs vectors of the same size: 0 0 1 :
vecdot needs vectors of the same size: 0 0 1 :
while executing
"error "vecdot needs vectors of the same size: $x : $y""
(procedure "vecdot" line 3)
invoked from within
"vecdot $normal [vecnorm $CC]"
(procedure "::membranetool_common::angle" line 11)
invoked from within
"::membranetool_common::angle $atomcoord1 $atomcoord2 $normal"
(procedure "::lipidtilt::tilt_lip" line 51)
invoked from within
"::lipidtilt::tilt_lip [array get lipid_array] $nleaf $atomselection $FILE $FILE_plot $lipids $f"
("uplevel" body line 2)
invoked from within
"uplevel $block"
("while" body line 4)
invoked from within
"while $expression {
set pwvar $f
eval $wrapcmd
uplevel $block
animate delete all
incr f $step
mol addfile $dcd first $f last $f waitfor all
..."
(procedure "::membranetool_common::for_frames" line 19)
invoked from within
"::membranetool_common::for_frames $dcdfile $from $to $step f $wrapcmd {
::lipidtilt::tilt_lip [array get lipid_array] $nleaf $atomselection $FILE ..."
(procedure "::lipidtilt::tilt" line 91)
invoked from within
"::lipidtilt::tilt -structure /home/sunidhi/RA/ABCA1/sim1/MD1_without_water.gro -trajectory /home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000...."
("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/MD1_without_water.gro -trajectory /home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt..."
("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/MD1_without_water.gro} -trajectory {/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc} ..."
("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)
Can anyone please help? Please.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Sunidhi ,
In the [GeneralRequirements] page, it is explained that, in some cases, a PDB or a GRO file cannot be used for computations as it does not contain connectivity information. At the end of that page, it is explained how to generate a PSF file, which is a source of connectivity data compatible with VMD, from a GROMACS TOP file.
Best regards,
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.
Dear Sunidhi ,
In the [GeneralRequirements] https://sourceforge.net/p/membplugin/wiki/GeneralRequirements/ page, it
is explained that is some cases a PDB or a GRO file cannot be used for
computations as it does not contain connectivity information. At the end of
that page it is explained how to generate a PSF file, which is a source of
connectivity data compatible with VMD, from a GROMACS TOP file.
Best regars,
Ismael.
I generated a psf file from my trajectory file (by converting one frame to pdb and then using the pdb to generate the psf). Even then the same error pops up:
Error:
vecdot needs vectors of the same size: 0 0 1 :
vecdot needs vectors of the same size: 0 0 1 :
Can you please help??
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
Your PSF have less atoms defined than atoms are in your XTC file. VMD requires that topology files (i.e PSF file) contain topology information for all the atoms in the coordinates files (i.e XTC file).
Please, regenerate your PSF files including all the topologies for all the atoms in your system or yout XTC file.
Best,
Ismael.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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.
Your PSF have less atoms defined than atoms are in your XTC file. VMD
requires that topology files (i.e PSF file) contain topology information
for all the atoms in the coordinates files (i.e XTC file).
Please, regenerate your PSF files including all the topologies for all the
atoms in your system or yout XTC file.
I have a system with a protein and a lipid membrane together. The membrane has 7 different lipid types but only POPC throws the following error while running MEMBPLUGIN:
Something went wrong.
Command: lipidtilt -structure /home/sunidhi/RA/ABCA1/sim1/MD1_without_water.gro -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 POPC.angles} -wrapcmd {pbc wrap -center bb -centersel membplugin_lipid -compound res}
Error:
vecdot needs vectors of the same size: 0 0 1 :
vecdot needs vectors of the same size: 0 0 1 :
while executing
"error "vecdot needs vectors of the same size: $x : $y""
(procedure "vecdot" line 3)
invoked from within
"vecdot $normal [vecnorm $CC]"
(procedure "::membranetool_common::angle" line 11)
invoked from within
"::membranetool_common::angle $atomcoord1 $atomcoord2 $normal"
(procedure "::lipidtilt::tilt_lip" line 51)
invoked from within
"::lipidtilt::tilt_lip [array get lipid_array] $nleaf $atomselection $FILE $FILE_plot $lipids $f"
("uplevel" body line 2)
invoked from within
"uplevel $block"
("while" body line 4)
invoked from within
"while $expression {
set pwvar $f
eval $wrapcmd
uplevel $block
animate delete all
incr f $step
mol addfile $dcd first $f last $f waitfor all
..."
(procedure "::membranetool_common::for_frames" line 19)
invoked from within
"::membranetool_common::for_frames $dcdfile $from $to $step f $wrapcmd {
::lipidtilt::tilt_lip [array get lipid_array] $nleaf $atomselection $FILE ..."
(procedure "::lipidtilt::tilt" line 91)
invoked from within
"::lipidtilt::tilt -structure /home/sunidhi/RA/ABCA1/sim1/MD1_without_water.gro -trajectory /home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000...."
("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/MD1_without_water.gro -trajectory /home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt..."
("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/MD1_without_water.gro} -trajectory {/home/sunidhi/RA/ABCA1/sim1/MD1_17_nopbc_norottrans_dt1000.xtc} ..."
("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)
Please check the following thread:
https://sourceforge.net/p/membplugin/discussion/general/thread/c5f77873/#4ac9/2b18
Ismael.
I did. But nothing mentioned in this, seems to solve the problem.
On Sun, 26 Apr 2020, 13:04 Ismael Rodriguez Espigares, ismresp@users.sourceforge.net wrote:
Last edit: Sunidhi 2020-05-04
Dear Sunidhi ,
In the [GeneralRequirements] page, it is explained that, in some cases, a PDB or a GRO file cannot be used for computations as it does not contain connectivity information. At the end of that page, it is explained how to generate a PSF file, which is a source of connectivity data compatible with VMD, from a GROMACS TOP file.
Best regards,
Ismael.
Related
Wiki: GeneralRequirements
Last edit: Ismael Rodriguez Espigares 2020-04-26
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.
On Sun, Apr 26, 2020 at 2:02 PM Ismael Rodriguez Espigares ismresp@users.sourceforge.net wrote:
Related
Wiki: GeneralRequirements
Hey Ismael
I generated a psf file from my trajectory file (by converting one frame to pdb and then using the pdb to generate the psf). Even then the same error pops up:
Error:
vecdot needs vectors of the same size: 0 0 1 :
vecdot needs vectors of the same size: 0 0 1 :
Can you please help??
Hi Sunidhi,
The root of the error is in here:
Your PSF have less atoms defined than atoms are in your XTC file. VMD requires that topology files (i.e PSF file) contain topology information for all the atoms in the coordinates files (i.e XTC file).
Please, regenerate your PSF files including all the topologies for all the atoms in your system or yout XTC file.
Best,
Ismael.
Did that. Yet another error popped up which I reported in another thread.
On Mon, May 11, 2020 at 6:03 AM Ismael Rodriguez Espigares ismresp@users.sourceforge.net wrote: