[gmx-users] various issues when simulating cholesterol membrane

Ayesha Fatima ayeshafatima.69 at gmail.com
Mon Sep 30 05:21:24 CEST 2019

Dear All,
It has been a futile effort so far when I want to just simulate a simple
cholesterol membrane. I checked the mailing list. but some how my issues
was not really answered.
So after following a few answers and solutions here and there, i would like
to as a few questions  which i cannot solve even after following the
solutions posted.
1. My cholesterol membrane was prepared usingthe CHARMM Membrane BUilder,
hence it sed the xharmm forcefield. There is only 1 charmm forcefield in
Gromacs 2019 Charmm27. so, I downloaded the forcefield and parameter files
Slipids_2016 from the http://www.fos.su.se/~sasha/SLipids/. I used the non
bonded and bonded forcefield parameters given as there is a unique hydrogen
named H3' which is not found in other forcefields such as Gromos53A6 or
Although when I used 54A7 parameterised cholesterol.itp from ATB server, i
got the error or naming mismatch which i thinks is because the number of
cholesterol atoms in the ATB file is only 31 while my pdb file has 74 atoms
per molecule and also the atom types are different.
If I use the normal charmm27 forcefield extended to BERGER lipids, error of
proper dihedrals, U-B atoms and i j parameters comes when it reads the
So when i will want to parametrise the protein, i will have issues or can i
use the same forcefield since the file does have the amino acid parameters
Kindly suggest  what can be the correct way?
Thank you
Ayesha Fatima

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