[gmx-users] grompp error in simulation of membrane protein.

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 7 12:08:59 CEST 2009

nitu sharma wrote:
> Hello justin ,
> thanks for ur previous suggestion . I am doing simulation of membrene 
> protein  , as u suggest in  previous mail to use gromos9653a6 forcefield 
> parameters  in topology file of protein+lipid bilayer.
> I have made topology accordingly like this-
> ; Include forcefield parameters
> #include "ffG53a6.itp"
> #include "lipid.itp"
> #include "dmpc.itp"

As I have said, time and time again, the above setup will likely give problems. 
  What you should do is append the relevant directives from lipid.itp into 
ffG53a6nb.itp and ffG53a6bon.itp, removing the section called ";; parameters for 
lipid-GROMOS interactions," as they pertain to ffgmx.

> [ molecules ]
> ; compound  #mols
> Protein_A    1
> Protein_B    1
> DMPC        128
> SOL        3552
> Na           1

This isn't going to work either, since Na corresponds to an ffgmx NA+ ion; you 
need NA+, which is the correct nomenclature for ffG53a6.

> But when I run the grompp command I got the error like this-
> Fatal error:
> Atomtype CA not found

Again, this is an ffgmx atom type, probably because you're using this hacked 
topology; including lipid.itp as is calls some ffgmx atom types.


> I have tried to solve this problem by adding CA atom with its mass  in 
> ffG53a6.atp file and atom CA with its all information ffG53a6nb.itp file 
> but even after doing this correction I am getting same error .
> Please Can u suggest me what should I have to do to solve this problem .
> I am a new gromacs user , I have done the simulation of protein and 
> lipid bilayer separetly but this type of problem didnot came so I have 
> no much idea .
> I am waiting for ur reply.
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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