Activity for MEMBPLUGIN
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Ismael Rodriguez Espigares posted a comment on discussion General Discussion
Dear Alain, The only thing that can be failing is the atomselection that selects the phosphate atoms in your simulation. Your are running membrane thickness tool with the default "name P" atomselection. Please, check that the phosphates in your simulation have as atom name "P", and that your structure (.gro) and trajectoriy (.xtc) files are loaded correctly by VMD, file paths E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro and E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.xtc...
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Alain Mutangana posted a comment on discussion General Discussion
I am trying to compute thickness but I am encoutering this issue. I have my system wrapped and when I put my topology resname detail, it still ives me this Something went wrong. Command: membranethickness -structure E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro -trajectory E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.xtc -from 0 -to last -step 1 -sel {name P} -o E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.thickness...
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Yes, that's it. But, the plane of the triad of atoms being parallel to the main plane of the membrane is not so important if the atoms of the triad from the same molecule are close to each other.
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Hossein Hajiabadi posted a comment on discussion General Discussion
Thank you Ismael! So, I should select an atom or a triad of atoms in the same membrane depth. Also, the plane of the triad of atoms must be parallel to the main plane of the membrane. Am I getting this right?
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The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (e.g. sterols) or a triad of atoms (e.g. phospho- or sphingolipids). The x and y coordinates of the former set of points are projected onto a plane delimited by the simulation box, which is subsequently divided into polygons through a ** Voronoi diagram** using the qvoronoi program from the...
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Hello everyone! APL analysis needs renames and a selection of atoms from each resname for each lipid type. But I'm not sure how to choose atoms for each lipid type. Apparently, it can be a single atom or a triad of atoms, but what atoms should I select for each lipid type? What are the circumstances for selecting atoms? How much does selecting atoms affect the final results? I really appreciate any help you can provide.
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Question about running MEMBPLUGIN in VMD Text Mode
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Please, write your questions in the "Discussion" section, and first read the wiki section. You would find there the commands for text mode. Also, you can run a computation using the GUI and the corresponding text command will be printed in the VMD terminal. Bests. Ismael.
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Zahra Aliakbartehrani created ticket #8
Question about running MEMBPLUGIN in VMD Text Mode
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Toni posted a comment on discussion External tools: Density Profile and Diffusion Coefficient
Sure, https://github.com/giorginolab/vmd_diffusion_coefficient/ And https://github.com/giorginolab/vmd_density_profile Il ven 6 mag 2022, 19:29 Robert Coffman korash@users.sourceforge.net ha scritto: Is there an updated link for these external tools? multiscalelab.org seems to be for sale. Welcome https://sourceforge.net/p/membplugin/discussion/external_tools/thread/067e0582/?limit=25#bed8 Sent from sourceforge.net because toni.giorgino@gmail.com is subscribed to https://sourceforge.net/p/membplugin/discussion/external_tools/...
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Robert Coffman posted a comment on discussion External tools: Density Profile and Diffusion Coefficient
Is there an updated link for these external tools? multiscalelab.org seems to be for sale.
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Uda Yuma Official posted a comment on a wiki page
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Nur Hanna Mardhiyyah posted a comment on discussion General Discussion
Oh my god. Yes, it is. I haven't checked it before. Thank you for your explanation, now I get it why it became like that. Apparently, that's because my residue names in atom selection didn't match with my residue names as lipid1. I think I should check it carefully beforehand. I will reply it again if I have another problem. Bless you.
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Dear Nur Hanna Mardhiyyah , It seems that your computation has produced an empty file with no data, that is why it cannot be plotted. Please, review and repeat your computation taking special care in providing apropiate atom selections and residue names and atom names (see [LipidTilt]). If you still have problems, please post here your terminal output just after running the computation of Lipid Tilt, including the commands that are printed in there. Best, Ismael.
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Hello. My name is Nur Hanna Mardhiyyah, majoring Chemistry at Diponegoro University, Indonesia. I'm still doing my final project and facing a problem. While I was plotting my P-N atom on Lipid-Tilt analysis, it got an error. It was okay on my cholesterol Lipid-Tilt analysis, but turned out error when I did it on my P-N atom Lipid-Tilt analysis. Please help me solve this problem. Thank you. Regards, Hanna. can't read "data_d": no such variable can't read "data_d": no such variable while executing...
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Thank you so much! I've been successfully calculate it. Bless you.
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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...
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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...
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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)
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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.
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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...
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Alexandre Suman de Araujo posted a comment on discussion General Discussion
Dear Ismael. Thank you for your prompt response and for considering my proposal for the future. Some time ago I calculated SCD using a script I've found on the web and I will try to change it to perform in the way I need. Regards. Alexandre
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Dear Alexandre, The current implementation of MEMBPLUGIN does not offer the option to update the atom selection on each frame for membrane SCD plugin. We will consider your new feature proposal of being able to enable and disable atomselection update in future releases. Best regards, Ismael Rodríguez Espigares.
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Hi all. I am trying to calculate the SCD of lipids near an adsorbed peptide (5 angstrons, for example). However, due to the bilayer's dynamic, the lipids around the peptide change every time and I need to update the selection on each analyzed frame. Is it possible to update the selection in SCD calculations with MEMBPLUGIN? Regards. Alexandre
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Also, could you provide the command that is printed in the terminal when you run the computation? Thanks.
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Dear Shashank Pant, First, I suggest that you better use the discussion forum, so other people experiencing the same problem can be aided with the resolution of your questions. Secondly, are you trying to measure the SCD of myristoyl tail attached to a protein residue? If the answer is afirmative, this is a case that we have not tested and we cannot answer why is failing right know. So, probably is going to take us some time to figure out what went wrong and even if this case is supported by our...
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Dear Shashank Pant, First, I suggest that you better use the discussion forum, so other people experiencing the same problem can be help with the resolution of your questions. Secondly, are you trying to measure the SCD of myristoyl tail attached to a protein residue? If the answer is afirmative, this is a case that we have not tested and we cannot answer why is failing right know. So, probably is going to take us some time to figure out what went wrong and even if this case is supported by our software....
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Shashank Pant created ticket #7
SCD of unnatural lipid tail
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Sunidhi posted a comment on discussion General Discussion
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: Hi Sunidhi, The root of the error is in here: 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...
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Hi Sunidhi, Please check this thread https://sourceforge.net/p/membplugin/discussion/plotting/thread/89e8f9c2/#0f5e/6bf1. It explains how to generate the image in postscript format. Best, Ismael.
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Hi Sunidhi, The root of the error is in here: 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...
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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...
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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 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...
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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...
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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. Alternatively, you may add any missing residue names to the "lipids" variable in the MEMBPLUGIN configuration file that you can...
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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...
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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...
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Hello Some output from MEMBPLUGIN like Membrane thickness --> average thickness plot have options of downloading the generated figure/image in different formats like postscript and xvg. But the average, bottom and top thickness maps generated from "Membrane thickness" are displayed just as images with title "tmap". I want to download these images in postscript format or high-dpi images. Kindly suggest how to do that.
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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??
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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: Please check the following thread: https://sourceforge.net/p/membplugin/discussion/general/thread/c5f77873/#4ac9/2b18 Ismael. Error while running Lipid Tilt angle using a GRO file (duplicated) https://sourceforge.net/p/membplugin/discussion/general/thread/1c7873b7fc/?limit=25#1c99 Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/membplugin/discussion/general/...
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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...
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This is the log file of the error: 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...
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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...
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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...
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Could post also the command that is printed in the terminal/cmd/tcl/tk console of VMD?
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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?
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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.
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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.
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Dear Sunidhi , In the [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.
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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 Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/membplugin/discussion/general/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
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I obviously did. But nothing mentioned in this, solves the problem! On Sun, 26 Apr 2020, 13:04 Ismael Rodriguez Espigares, ismresp@users.sourceforge.net wrote: Please check the following thread: https://sourceforge.net/p/membplugin/discussion/general/thread/c5f77873/#4ac9/2b18 Ismael. Error while running Lipid Tilt angle using a GRO file (duplicated) https://sourceforge.net/p/membplugin/discussion/general/thread/1c7873b7fc/?limit=25#1c99 Sent from sourceforge.net because you indicated interest in...
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Dear Victor Daniel, Probably, that specific frame might be tricky for qvoronoi tessellation for some reason. Could you send us your PSF file and an XTC file with this frame2105, please? Otherwise, it will be difficult to replicate the error and check exactly what is failing. In any case, you can just run the analysis from the frame 0 to 2014, and a second one from 2016 to 4999. Thanks.
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Please check the following thread: https://sourceforge.net/p/membplugin/discussion/general/thread/c5f77873/#4ac9/2b18 Ismael.
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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 deafult list and you'll need to setup a custom residue name list in the main membplugin window.
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Could please check if output files are not empty?
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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...
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victor daniel aldas bulos posted a comment on discussion General Discussion
I've already use the tool for the same membrane to analyze the production phase. Some results made me want to analyze the equilibration phase as well. I'm using the same triad of atoms as in the production analysis. The program runs until the frame 2105 (there are 5000 in total) and then shows this error: Something went wrong. Command: lipidarea -structure /home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7 -trajectory /home/bulos/Desktop/respaldo/membrana/memtotal.dcd -triatom {{"POPE"...
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Dear Sunidhi, Could you please send me the .orderparSCD and the .orderparSCD_plot~ files generated by Membrane SCD (the last one might be marked as a hidden or system file. You might have to enable "show hidden files" feature in your file browser)?
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I tried using Area per lipid and after giving in gro and xtc files, this is the error encountered while trying to plot the result. Please help. can't read "data_d": no such variable can't read "data_d": no such variable while executing "dict for {l lipid_d} $data_d { set Xlist {} set Ylist {} set Errlist {} dict for {f frame_d} $lipid_d { set input_l {} set nleaf 0 di..." ("area" arm line 36) invoked from within "switch -- $dataswitch { area { set stdflag 0 set stderrflag 0 set residues_num [lsearch...
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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"...
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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"...
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Ramon Guixà-González posted a comment on discussion General Discussion
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
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Albert posted a comment on discussion General Discussion
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"...
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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...
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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.
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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...
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Pacho Ramos posted a comment on discussion General Discussion
OK, thanks a lot for the clarification
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Dear Pacho, Currently, there is no way to overcome these 3 cases with MEMBPLUGIN. We will update the tutorial and wiki page if we manage to address those cases in the future. Best regards, Ismael.
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Hello, I discovered your plugin while reading papers like: https://pubs.rsc.org/en/content/articlelanding/2017/CP/C7CP01941F#!divAbstract that use your tool to analyze simulation involving peptides but, when I read your tutorial, I found that, supposedely, membplugin doesn't handle that cases (simulations involving anything else than lipids): https://sourceforge.net/projects/membplugin/files/Tutorial/intro_SDPCandCHOL_v3.pdf/download Second point, page 2: "Do not use or use the MEMBPLUGIN with caution...
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Anjela Manandhar posted a comment on discussion General Discussion
Thank you for the explanation Toni. Sincerely, Anjela Manandhar Graduate Student Biochemistry Program Graduate Center, City University of New York 365 Fifth Avenue, NY-10016, USA On Mon, Jul 29, 2019 at 3:32 AM Toni tigio@users.sourceforge.net wrote: Dear Anjela, our analysis (hence the code) assumes an “almost planar” bilayer. Yours is pretty strongly curved. What’s happening (as far as I can tell) is that the plane-fitting is failing and so is the upper/lower lipid assignment. Maybe some future...
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Dear Anjela, our analysis (hence the code) assumes an “almost planar” bilayer. Yours is pretty strongly curved. What’s happening (as far as I can tell) is that the plane-fitting is failing and so is the upper/lower lipid assignment. Maybe some future version… Best TG
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Hi Ismael, I am calculating total thickness. When I calculate just the average thickness, I am still getting high values (~166A) and thickness map (with total thicknes) have similar values as well. Please let me know if more information is required. Thank you. Sincerely, Anjela Manandhar Graduate Student Biochemistry Program Graduate Center, City University of New York 365 Fifth Avenue, NY-10016, USA On Thu, Jul 25, 2019 at 5:19 PM Ismael Rodriguez Espigares ismresp@users.sourceforge.net wrote: Dear...
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Dear Anjela, In order to help you, could you tell me if you had computed the deformation map using the total thickness or the leaflet deformation option? You can find our definition of leaflet deformation in [MembraneThickness] and how it is computed in this thread. If you used the leaflet deformation option, the results look reasonable to me as the most deformed region of the membrane is the most curved region. Best regards, Ismael.
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Dear Angela, In order to help you, could you tell me if you had computed the deformation map using the total thickness or the leaflet deformation option? You can find our definition of leaflet deformation in [MembraneThickness] and how it is computed in this thread. If you used the leaflet deformation option, the results look reasonable to me as the most deformed region of the membrane is the most curved region. Best regards, Ismael.
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Hi, I am trying to use Membplugin for the membrane thickness analysis. My membrane deforms, bends/curves during simulation. When I calculate deformation map, it shows curved area to be thickest (almost double the average thickness of the membrane). Can you please help me with this. Thank you. Sincerely, Anjela
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DX file contains X,Y,Z and U values, where U is a function of X,Y and Z. X, Y and Z are spatial coordinates and U(X,Y,Z) are the written values in the file (thickness or deformation in this case). X, Y and Z coordinates are represented as 3D ordered regular-spaced grid points, but they are not directly written in the file. xdel, ydel and zdel are the spacing between points on each one of the axes and they are written in the header of the file. Minima of X, Y and Z (xorg, yorg and zorg) is also writen...
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Dear Yasser Almeida, zn = 2 and zdel = 2.0 is hardcoded to workarround the fact that DX files does not support 2D data and to ease visualization in VMD by setting the Z axis width of the represented VOLMAP to 2 angstroms. The value of thickness/deformation is repeated with identical value "zn = 2" times along the z axis.
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Yasser Almeida posted a comment on discussion Data plotting suggestions
Dear Ismael, I am affraid I still don't get the idea of the format. Attached is my .dx file. It contains 2x the values. My first basic question is, are those all Z values? If I split the file, the values of the second half is not identical to the first. Is there a way to get the X, Y, (averaged) Z values directly? Regards
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Dear Yasser Almeida, zn = 2 and zdel = 2.0 is harcoded to workarround the fact that DX files does not support 2D data and to ease visualization in VMD by setting the Z axis width of the represented VOLMAP to 2 angstroms. The value of thickness/deformation is repeated with identical value "zn = 2" times along the z axis.
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Dear Yasser Almeida, zn = 2 and zdel = 2.0 is harcoded to workarround the fact that DX files does not support 2D data and to ease visualization in VMD by setting the thinkness of the represented VOLMAP to 2 angstroms. In the case of the membrane thickness tool, the value of thickness/deformation is repeated with identical value "zn = 2" times along the z axis.
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Dear Sneha, Membrane thickness image export option is not implemented yet, but running the following commands while having the colour map window opened in a TK console (in Extensions menu) should generate a save as postcript file dialog: set tmap_canvas .mtthicknessgui.tmap.canvas; lassign [split [lindex [split [winfo geometry $tmap_canvas] +] 0] x] width height; ::membranetool_common_gui::save_plot $tmap_canvas $width $height; Regarding the .dx file, it contains the same data as the colour map as...
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Thank you, for the explanation. I have a case were I get zn = 2, so I have two grids. Any ideas?
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unusual APL behaviour
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For obtaining the number of lipids in the system and indentifying which residues are in the upper and lower leaflet, the internal VMD property "residue" is used. This property identifies residues automatically using connectivity. In this specific case, VMD has failed to guess connectivity creating hundreds of fragments with individual "residue" numbers. Total area per lipid = Total area / number of lipids in the system Hence, the mess in the Total area per lipid is caused by unreliable connectivity...
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Updated wiki to add in requeriments that extremly deformed membranes may lead to leaflet assignment issues.
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Updated wiki to add in requeriments that extremly deformed membrains may lead to leaflet assignment issues.
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AreaPerLipid
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GeneralRequirements
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We cannot reproduce the error without the data. Probably, it is a qvoronoi tesselation error that for some sets of values it is not possible to tesselate.
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We cannot reproduce the error without the data. Probably, it is a qvoronoi tesselation error that for some sets of values it is not posible to tesselate.
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Hector Martinez-Seara Monne modified a comment on ticket #6
After analyzing the problem a bit I see two different issues here. 1) The system present significant curvature That makes the selection method of which lipids are in the upper and lower leafleat to fail. I think that this is a know problem of our sofware and we should probably warn the users better. 2) The calculation of the total area per lipid fails While the are per lipid (POPC) look correct, they are small because of the curvature, the issue is that the total is a mess. At this point, I do not...
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After analyzing the problem a bit I see two different issues here. 1) The system present significant curvature That makes the selection method of which lipids are in the upper and lower leafleat to fail. I think that this is a know problem of our sofware and we should probably warn the users better. The calculation of the total area per lipid fails While the are per lipid (POPC) look correct, they are small because of the curvature, the issue is that the total is a mess. At this point, I do not understand...
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daniel holy modified a comment on ticket #6
The system is a bilayer of 880 POPC molecules. 480 POPC molecules are restrained, enforcing a positive curvature (designated in the structure file as 'POPP'), the rest are free to move. I am including my structure file, short trajectory of three frames, screnshot of the settings and a file with the total area showing, that the program doesn't select the same number of lipids for each leaflet every time.
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The system is a bilayer of 880 POPC molecules. 480 POPC molecules are restrained, enforcing a positive curvature (designated in the structure file as 'POPP'), the rest are free to move. I am including my structure file, short trajectory of three frames, screnshot of the settings and a file with the total area showing, that the program doesn't select the same number of lipids for each leaflet every time.
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unusual APL behaviour
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Dear Muthukumaran R, The most likely explanation for the error that you found, taking into account that you are using a GRO file as topology file, is that VMD is not guessing correctly the connectivity of your POPE molecules and they get broken in some point. These also might happen when using PDB files as topology. Also, your system must be wrapped in a way that molecules in PBC bounderies are not broken. Please, check requeriments regarding wrapping and loading topology in VMD at [GeneralRequirements]...
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