Non-protein non-nucleic acid membrane system

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1

GROMACS version:
GROMACS modification: Yes/No
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Hi! I’m trying to run a simple membrane simulation, solely simulating lipids. However, I’m having trouble parametrizing the lipids. I’ve generated a modified Gromos54a7 ff with my molecule through ATB3.0 and have also gotten its molecular topology file. However, I’m a little confused how I should be doing the #include statements for my system.

I currently have three main things:
lipid.itp
topol.top
modified_gromos54a7_atb.ff

Within my topol.top file I have #include statements for the forcefield.itp, spc.itp, ions.itp within the modified.ff folder, as well as my lipid.itp.

Within my lipid.itp file, i just have an include statement including the forcefield folder which is quite literally:
“#include modified_gromos54a7_atb.ff”

However, throughout the steps before minimization, like solvation and adding ions, I’ve been getting this one message

“Unknown error, perhaps your text file uses wrong line endings? - File
modified_gromos54a7_atb.ff, line 0”

which makes me suspect I wrote the files incorrectly because it’s a directory. I am an utterly confused undergrad with no previous MD sim experiences. I would greatly appreciate any advice in troubleshooting!

2

Dear @lipidsolidarity

I think the problem is here

as you are including a directory, but you should include files, that is, something like

#include "./modified_gromos54a7_atb.ff/forcefield_parameters.itp"
#include "./modified_gromos54a7_atb.ff/lipid_parameters.itp"
...
...
3

Hi, it turns out it was an #end if vs #endif typo. Thank you for your help, though!