On 11/11/11, LindaSong <wlsongli...@gmail.com> wrote: > 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
I thought said you had 256 molecules of lipid... > > > 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?). PME does calculate a long-range interaction. From your report, I don't think you are actually using PME, but it is probably irrelevant for membrane insertion. > 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 Use of -maxwarn is a bad habit unless you really know what the problem is and the consequences of ignoring it... > > > 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. So there is something catastrophically wrong with the starting configuration... > > > > 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 why in the topology file it says only 1 POPC? This is what I got > when I used pdb2gmx to generate the topology file for POPC. > It's hard to say without knowing what you did with pdb2gmx. You should be able to take your structure file with protein and POPC overlaid, pass that to pdb2gmx and get a correct .top. Depending on how the different POPC molecules are differentiated, you may need to choose pdb2gmx -chainsep differently. Mark
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