[gmx-users] Re: Problems with g_membed tools

LindaSong wlsonglinda at gmail.com
Fri Nov 11 03:30:00 CET 2011

Thank you for reply. I am sorry I didn't apply more information

There are only protein and lipids in my system now. I used the CHARMM ff. The topology is like this:
    [ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_A2    1
POPC                1

In the grompp step, I used PME to calculate the electrostatic interaction, set the energy group to be Protein and the energy group exclusion to be 'Protein Protein'. I ignored the warning that grompp tells PME not calculating the long-distance interaction,because I think the long-distance interaction does not matter in this membrane insertion (Is this right?). And then get the output tpr file. command line like this:

                grompp -f membed.mdp -c complex_noLIG_m.pdb -p topol.top -o membed.tpr -maxwarn 1

Then I used the generated tpr file in the g_membed, command line like this:

                 g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000

I selected the Protein to be embeded in and POPC the protein be embeded into;

Then the g_membed tells:
      The estimated area of the protein in the membrane is 11.745 nm^2

      There are 1 lipids in the membrane part that overlaps the protein.
      The area per lipid is inf nm^2.
      Maximum number of lipids that will be removed is 0.

      Will resize the protein by a factor of 0.100 in the xy plane and 1.000 in the z direction.
     This resizing will be done with respect to the geometrical center of all protein atoms
      that span the membrane region, i.e. z between 2.510 and 7.767

       Embedding piece 0 with center of geometry: 5.261230 5.247513 5.138600

    Program g_membed, VERSION 4.5.3
    Source code file: gmx_membed.c, line: 688

       Fatal error:
      Trying to remove more lipid molecules than there are in the membrane
       For more information and tips for troubleshooting, please check the GROMACS
       website at http://www.gromacs.org/Documentation/Errors

So why the maximum number of lipids to be removed is 0? And I don't understand whyin the topology file it says only 1 POPC? This is what I got when I used pdb2gmx to generate the topology file for POPC.

Thanks again.

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