[gmx-users] lipid tutorial problem

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 13 14:10:14 CET 2012

prashant kurkute wrote:
> Dear all,
> I am very new to GROMACS.
> The my problem may be a very basic and stupid but very big for me!!!!!!..
> I am performing Justin Lemkul  Lipid tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
> and I am upto the 3rd stage.
> But after  giving following command
> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
> I got the error like
> Fatal error:
> Atomtype CA not found
> Please give me some valuable suggetion.

Read more closely:


"In the [ nonbond_params ] section, you will find the line ";; parameters for 
lipid-GROMOS interactions." Delete this line and all of the subsequent lines in 
this section. These nonbonded combinations are specific to the deprecated ffgmx 
force field."

The CA atom type is from ffgmx, and hence the error.



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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