[gmx-users] grompp error in running simultion of membrane protein with lipid bilayer

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 3 12:30:01 CEST 2009

nitu sharma wrote:
> Dear all,
>                    I am trying to do simulation of membrane protein with 
> lipid bilayer  for this I have made topology file like this-
> ; topology for tap in 128 dmpc lipids plus water.
> ; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with 
> pdb2gmx, starting
> ; with a pdb file of tap transporter.
> ; make sure lipid.itp,dmpc.itp and rr1.itp are in a location where
> ; grompp can find them (GMXLIB, current directory, or directory given in
> ; the .mdp file with the include option.
> #include "ffoplsaa.itp"
> #include "lipid.itp"
> #include "dmpc.itp"

This will not work.  I said the exact same thing to someone else not two or 
three days ago.  You cannot combine OPLS-AA with the standard Berger lipid 
parameters; the Berger atom types are for use with a Gromos force field.

You have three options:

1. Use a Gromos force field variant.  You still can't simply #include 
"lipid.itp," however, you will have to append the relevant directives to the 
ff*nb.itp and ff*bon.itp and use these modified files.

2. Modify lipid.itp to be in accordance with OPLS-AA conventions.  Chris Neale 
has posted a detailed procedure to do this; search the list archive.

3. Use the self-consistent Gromos96 53a6 force field parameters that have been 
uploaded to the Users' Contributions section of the website.

The choice is up to you, based on which setup you think is best for your system.

> when I am trying to run grompp after solvating the system I am getting 
> error like this-
> Program grompp, VERSION 4.0.3
> Source code file: toppush.c, line: 843
> Fatal error:
> Atomtype C not found
> --------------------------

Right, do you see atomtype "C" anywhere in ffoplsaa.atp?  This atomtype belongs 
to a Gromos force field.


> my command  line like this-
> grompp -f em.mdp -p rr1-dmpc.top -c solvated-tapp-mod.pdb -o tapp-mod-em.tpr
>  if anyone know about this please suggest me right thing to do.
> thanks.
> Nitu Sharma
> School of life sciences
> Jawaherlal Nehru University
> New Delhi India
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list