11 November 2018 1 10K Report

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)

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