How to build topology for the whole DGDG membrane?
I created DGDG (Digalactosyldiacylglycerol) membrane from scratch. I created DGDG molecule in Pymol. Then I rotate this molecule to have my acyl chain along z-axis. Then I created 8x8 down layer and rotated each lipid along z-axis I also created up-layer. Fuse layer into membrane put water in both side of membrane. Now I have a problem how to build topology, because I use OPLS-AA force field and there is no DGDG molecule in forcefield database, so I try to use TopolGen, Topolbuild, LigParGen to create topology. It was easy to use LigParGen to generate topology for one molecule and minimize energy (I have only WARNING 1 [file DGDG6.top, line 23]:
148 non-matching atom names
atom names from DGDG6.top will be used
atom names from DGDG5.gro will be ignoredWarning: atom name 15 in DGDG6.top and DGDG5.gro)
But LigParGen create topology only for molecule which have not more than 200 atoms, not whole membrane.
I try tu use Topolbuild. I create my file membrane_box.mol2 (open pdb file in Avogadro and save in Avogadro in .mol2 format). But when I write this:
./topolbuild -n membrane_box -dir usr/share/gromacs/top/oplsaa.ff -ff oplsaa
I have
Fatal error.
Source code file: readmol2.c, line: 639
Incomplete mol2 file after bonds record.
I also try to use
TopolGen
I have my pdb file, so I write:
perl topolgen_1.1.pl -f membrane_box.pdb -o membrane.itp -type itp
but I have
Cannot open "section_atoms_final" while writing output: No such file or directory
How to manage this problem?
I think also about to add topology of my DGDG molecule into a force field, because LigParGen, Topolbuild and TopolGen doesn't work.
This is my files:
DGDG12.pdb - My lipid which was construted in Pymol
membrane_box.gro - my whole membrane with water
membrane_box_avogadro.mol2 - membrane in .mol2 format
topol.top - topology, but I dont have my .itp file with topology I have only UNK.itp, but this is only one molecule
UNK.itp - topology of one DGDG molecule (created in LigParGen)
Dear Jakub,
As far as I know, CHARMM is much more commonly used than OPLS for membrane simulations, and here the typical system-building routine is as simple as going through several input preparation steps in the online tool Membrane Builder (http://www.charmm-gui.org/?doc=input/membrane).
You can prepare a membrane-only system composed of DGDG by choosing Glycolipids -> Add glycolipid, and then defining the DGDG molecule in the popup window. You'll get a solvated system ready for equilibration, along with properly formatted Gromacs input files.
I absolutely agree with Nebojša that in the longer run it's key to understand what exactly your simulation software is doing, and online tutorials will sure help you, but it might also help to start with something that is (more or less) guaranteed to work properly.
Have a look at https://www.frontiersin.org/articles/10.3389/fpls.2018.00126/full
Article Digalactosyldiacylglycerol is a Major Glycolipid in Floral O...
http://www.plantphysiol.org/content/114/4/1493
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