<DIV> </DIV><DIV> </DIV><SPAN>On 11/11/11, <B class=name>LindaSong </B><wlsonglinda@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:76d3e0a9.38b8.1339075d383.Coremail.wlsonglinda@gmail.com type="cite"><SPAN style="FONT-SIZE: 18px">Thank you for reply. I am sorry I didn't apply more information<br /><br />There are only protein and lipids in my system now. I used the CHARMM ff. The topology is like this:<br /> <SPAN style="FONT-SIZE: 13px"> [ molecules ]<br />; Compound #mols<br />Protein_chain_A 1<br />Protein_chain_A2 1<br />POPC 1</SPAN></SPAN></BLOCKQUOTE>
<DIV> </DIV><DIV>I thought said you had 256 molecules of lipid... </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:76d3e0a9.38b8.1339075d383.Coremail.wlsonglinda@gmail.com type="cite"><SPAN style="FONT-SIZE: 18px"><br /><br />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?).</SPAN></BLOCKQUOTE>
<DIV> </DIV><DIV>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. </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:76d3e0a9.38b8.1339075d383.Coremail.wlsonglinda@gmail.com type="cite"><SPAN style="FONT-SIZE: 18px"> And then get the output tpr file. command line like this:</SPAN><br /><br /> grompp -f membed.mdp -c complex_noLIG_m.pdb -p topol.top -o membed.tpr -maxwarn 1</BLOCKQUOTE>
<DIV> </DIV><DIV>Use of -maxwarn is a bad habit unless you really know what the problem is and the consequences of ignoring it... </DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:76d3e0a9.38b8.1339075d383.Coremail.wlsonglinda@gmail.com type="cite"><br /><br /><SPAN style="FONT-SIZE: 18px">Then I used the generated tpr file in the g_membed, command line like this:<br /></SPAN><br /> g_membed -f membed.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000<br /><br /><SPAN style="FONT-SIZE: 18px">I selected the Protein to be embeded in and POPC the protein be embeded into;<br /></SPAN><br /><SPAN style="FONT-SIZE: 18px">Then the g_membed tells:</SPAN><br /> The estimated area of the protein in the membrane is 11.745 nm^2<br /><br /> There are 1 lipids in the membrane part that overlaps the protein.<br /> The area per lipid is inf nm^2.<br /> Maximum number of lipids that will be removed is 0.</BLOCKQUOTE>
<DIV> </DIV><DIV>So there is something catastrophically wrong with the starting configuration...</DIV><DIV> </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:76d3e0a9.38b8.1339075d383.Coremail.wlsonglinda@gmail.com type="cite">
<DIV style="LINE-HEIGHT: 1.7; FONT-FAMILY: arial; COLOR: #000000; FONT-SIZE: 14px"><br /><br /> Will resize the protein by a factor of 0.100 in the xy plane and 1.000 in the z direction.<br /> This resizing will be done with respect to the geometrical center of all protein atoms<br /> that span the membrane region, i.e. z between 2.510 and 7.767<br /><br /> Embedding piece 0 with center of geometry: 5.261230 5.247513 5.138600<br /><br /><br /> -------------------------------------------------------<br /> Program g_membed, VERSION 4.5.3<br /> Source code file: gmx_membed.c, line: 688<br /><br /> Fatal error:<br /> Trying to remove more lipid molecules than there are in the membrane<br /> For more information and tips for troubleshooting, please check the GROMACS<br /> website at http://www.gromacs.org/Documentation/Errors<br /> -------------------------------------------------------<br /><br /><SPAN style="FONT-SIZE: 18px">So why the maximum number of lipids to be removed is 0? And I don't understand why </SPAN><SPAN style="FONT-SIZE: 18px">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.</SPAN></DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>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.</DIV><DIV> </DIV><DIV>Mark</DIV>