[gmx-users] various issues when simulating cholesterol membrane

Justin Lemkul jalemkul at vt.edu
Mon Sep 30 14:13:52 CEST 2019

On 9/29/19 11:21 PM, Ayesha Fatima wrote:
> 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

Don't use CHARMM27; it's an outdated force field. CHARMM-GUI should give 
you all the necessary GROMACS inputs (topology, .mdp, etc) as well as 
the CHARMM36 force field. Use CHARMM36.


> 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
> 54A7.
> 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
> cholesterol.itp.
> 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
> also?
> Kindly suggest  what can be the correct way?
> Thank you
> Regards
> Ayesha Fatima


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129


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