Activity for Ismael Rodriguez Espigares
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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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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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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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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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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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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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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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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 RodrÃguez Espigares.
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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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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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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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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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Add close thread button
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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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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 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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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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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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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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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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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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Home
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I have no experience with cardiolipins, but probably taking the atom names for PMCL by doing an analogy among two phospholipids and PMCL could be a good approach. This should result into a set of 6 atom names ("C12 CA1 CB1 C32 CC1 CD2" in CHARMM) for the resname "PMCL" . C12 = C32 = phospholipid C2 CA1 = CC1 = phospholipid C21 CB1 = CD1 = phospholipid C31 Maybe, you can add extra atoms that are usually in the same plane and in the rigid region of the lipid. The objective here is that the selected...
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Dear Physics, 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 frame 920, please? Otherwise, it will be difficult to replicate the error and check exactly what is failing. Thanks.
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ScdOrderParameter
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ScdOrderParameter
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ScdOrderParameter
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ScdOrderParameter
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ScdOrderParameter
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SOPS seems to be the one giving trouble. Did you rename your system in a way that atoms of one phophoslipid molecule only has only 1 unique residue name and each atom has a unique atom name? If so, please, use de following atomselection: "resname SOPS", and copy paste the output of the VMD terminal/console here. PS. Is VMD assigning correctly the bonds for you lipids molecules? If not, you would need to generate a PSF from your gromacs topology.
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SOPS seems to be the one giving trouble. Did you rename your system in a way that atoms of one phophoslipid molecule only has only 1 unique residue name and each atom has a unique atom name? If so, please, use de following atomselection: "resname SOPS", and copy paste the output of the VMD terminal/console here.
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Upvote #164 Modify the title of a forum thread.
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Upvote for #164 Modify the title of a forum thread.
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Maybe we should upvote #164 Modify the title of a forum thread. I think this post now is a duplicate of #164.
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I would recommend to give the feature to the Topic creator and to moderators and admins.
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It would be interesting to give authors and moderators the functionality to change Topic subjects (titles). Authors not always write the most descriptive titles (e.g. "please, help!"). Then, it is hard for users to search throught previous posts for finding an already proposed solution for their problem.
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Dear MEMBPLUGIN users, If you are experiencing installation problems, please, follow installation instructions in wiki:Installation. Please, read carefully and follow those instructions. Then, if you are still experiencing problems, please provide in your posts: Version of VMD. Path to VMDDIR. See wiki:Troubleshooting Copy and paste to your post VMD output from Command Promp / terminal window including any VMD errors. Windows users see How to copy text from Microsoft Windows Command Prompt Copy and...
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Dear MEMBPLUGIN users, If you are experiencing installation problems, please, follow installation instructions in wiki:Installation. Please, read carefully and follow those instructions. Then, if you are still experiencing problems, please provide us in your posts: Version of VMD. Path to VMDDIR. See wiki:Troubleshooting Copy and paste to your post VMD output from Command Promp / terminal window including any VMD errors. Windows users see How to copy text from Microsoft Windows Command Prompt Copy...
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Dear amruta, installation instructions in wiki:Installation have been tested on Windows. Please, read carefully and follow those instructions. Then, if you are still experiencing problems, please provide us: Version of VMD Path to VMDDIR. See wiki:Troubleshooting Copy and paste VMD output in the cmd text/terminal window including any VMD errors to your post. See How to copy text from Microsoft Windows Command Prompt Copy and paste whole VMD output in the cmd text/terminal window just after VMD has...
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Troubleshooting
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Troubleshooting
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Troubleshooting
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Troubleshooting
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Troubleshooting
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Installation
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Installation
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Installation
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Dear Rabeta Yeasmin, As far as I know, APBS is not a visualitzation program. It computes electrostatics for structural protein models and other force-field defined molecules and uses DX files as output. Please read these thread about ploting MEMBPLUGIN thickness results. I hope this helps.
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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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I've check the source code of MEMBPLUGIN and this is how xorg, yorg and zorg are computed: xorg = min(x) of the first selected frame. yorg = min(y) of the first selected frame. x = x coordinates of the leaflet in the atom selection for deformation or for the two bilayers in the atom selection for thickness. y = y coordinates of the leaflet in the atom selection for deformation or for the two bilayers for thickness. zorg = average of zmid_int across frames for deformation or zmid of the last selected...
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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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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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I've check the source code of MEMBPLUGIN and this is how xorg, yorg and zorg are computed: xorg = min(x) of the first selected frame. yorg = min(y) of the first selected frame. x = x coordinates of the leaflet in the atom selection for deformation or for the two bilayers in the atom selection for thickness. y = y coordinates of the leaflet in the atom selection for deformation or for the two bilayers for thickness. zorg = average of zmid_int across frames for deformation or zmid of the last selected...
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According to MEMBPLUGIN defaults (used in our paper (doi:10.1093/bioinformatics/btu037)) and by analogy, selections for phospholipids and sphingolipids consist on the following 3 atoms: C2 (the middle one) of the glicerol part in phospholipids or the C2 (bound to the amide bond of the acyl-chain 2) of the sphingosine part. C21: the first carbon of the acyl-chain 2 (the one forming part of the carbonyl group). C31: the first carbon of the acyl-chain 3 for phospholipids (not sphingolipids). C3: of...
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According to MEMBPLUGIN defaults (used in our paper (doi:10.1093/bioinformatics/btu037)) and by analogy, selections for phospholipids and sphingolipids are the following 3 atoms: C2 (the middle one) of the glicerol part in phospholipids or the C2 (bound to the amide bond of the acyl-chain 2) of the sphingosine part. C21: the first carbon of the acyl-chain 2 (the one forming part of the carbonyl group). C31: the first carbon of the acyl-chain 3 for phospholipids (not sphingolipids). C3: of the sphingosine...
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According to MEMBPLUGIN defaults (used in our paper (doi:10.1093/bioinformatics/btu037)) and by analogy, selections for phospholipids and sphingolipids are the following 3 atoms: C2 (the middle one) of the glicerol part in phospholipids or the C2 (bound to the amide bond of the acyl-chain 2) of the sphingosine part. C21: the first carbon of the acyl-chain 2 (the one forming part of the carbonyl group). C31: the first carbon of the acyl-chain 3 for phospholipids (not sphingolipids). C3: of the sphingosine...
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AreaPerLipid
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According to MEMBPLUGIN defaults (used in our paper (doi:10.1093/bioinformatics/btu037)) and by analogy, selections for phospholipids and sphingolipids are the following 3 atoms: C2 (the middle one) of the glicerol part in phospholipids or the C2 (bound to the amide bond of the acyl-chain 2) of the sphingosine part. C21: the first carbon of the acyl-chain 2 (the one forming part of the carbonyl group). C31: the first carbon of the acyl-chain 3 for phospholipids (not sphingolipids). C3: of the sphingosine...
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Definition is available at https://sourceforge.net/p/membplugin/wiki/MembraneThickness/ .
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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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Yes, that is the expected output. The only thing is that it is highly recommended to add only absolute paths (begining with backslash "/") when using "lappend auto_path" command as changing the working directory could make the packages stop working.
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OK. Please, run again VMD (preferably version 1.9.3) in a terminal and open a TK console (Extensions --> TK Console) . Then, run the following commands in the TK Console and paste here any output printed in the TK console or in the linux terminal after running those commands. Paste also the commands with the actual paths that you used: puts $env(VMDDIR); # this 'VMDDIR' is literal, do not replace lappend auto_path /path/to/membplugin-release-1.x/membplugin1.x; # is a directory source /path/to/membplugin-release-1.x/loadmembplugin.tcl;...
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