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"...

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...

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...

Following the tutorial of MEMBPLUGIN, I selected both "sn-2" and "sn-1" in the "acyl...

Thank you for such detailed comments. If I understand correctly, if we would like...

great, thanks alot. The problem solved now.

Hello: I am using autogrow from new molecules design. In my original protein pdb...

Hello: I found that Autogrow is using Autodock Vina for the docking process. However,...