[gmx-users] Simulation of POPC in water using CHARMM27

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri May 11 17:43:14 CEST 2012

Dear Anirban,
No, I have not done. Because I didn't know I need Berger lipids for this simulation. 

Thanks for you reply,

 From: Anirban <reach.anirban.ghosh at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, May 11, 2012 8:10 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27

On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

Dear gmx users,
>I'm going to simulate the POPC in water.
>I downloaded required files in Tielman site and made the .top file. Then included the CHARMM27.ff in the .top file.
>When I run the grompp I get the fatal error as below:
>Atomtype CB not found
>I have done the same with gromos87.ff . But I didn't see any error.
>What's the problem?
>Anybody may suggest me how to solve this problem? Is this because of the forcefield? Or something in .top file goes wrong?

Have properly edited the CHARMM27 bonded and nonbonded .itp files to include the Berger lipid parameters and have you included the POPC topology? You can follow this tutorial to get an idea:


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