[gmx-users] Need help!!!

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 2 15:10:35 CEST 2010

praba vathy wrote:
> Hi,
> I am using simulation for a membrane protein.
> So i have downloaded the dppc.pdb along with it's topology files.
> I have used the following steps for the simulation (Based on the link:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).
> We have used the commands and steps as described in the above link.
> But we have got a fatal error (Atom type C not found) while running this 
> command,
> grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp <http://em.tp>
> I cant sort out this problem.
> Please anybody help me to sort out this problem.
> Awaiting for your valuable replies.

This is a very different error than what you reported before, and since dppc.itp 
does not contain atom type "C" the error indicates (once again) that you have 
incorrectly constructed the ffG53a6nb_lipid.itp file that is described in the 
tutorial.  Please start over and follow the instructions closely.  If you do so, 
you will not get errors about missing atom types.


> Praba


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


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