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.
Linda
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