Hello Shamik,<br><br>Going through the membrane protein tutorial will help you to get answers to these questions.<br>The lipid.itp file has to be modified and edited depending on the force fields being used like opls force field or the gromos96 force field. Popc.itp file should also be included in order to include the topology for the POP residues. lipid.itp file is used to include more of interaction parameters.<br>
<br>Regards,<br>Pawan<br><br><div class="gmail_quote">On Fri, May 22, 2009 at 4:58 PM, Samik Bhattacharya <span dir="ltr"><<a href="mailto:samikbhat@yahoo.co.in">samikbhat@yahoo.co.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div>Thanks pawan, for helping.... but one problem still remains that is how to incorporate the .itp file inside the topology file???? and which .itp file should i include is it the lipid.itp orr POPC.itp??<br>
thanx for your help<br>Shamik<div class="im"><br><br><br><br><br><br>Greetings from Pawan.<br>Topologies for lipids like POP are not available in the topology database in gromacs.<br>So the starting point would be to generate a topology and a gro file for the protein alone as such and then edit the topology to include the .itp files as specifically needed for the lipids.<br>
<br>Regards,<br>Pawan<br><br></div><div class="gmail_quote"><div class="im">On Fri, May 22, 2009 at 4:42 PM, Samik Bhattacharya <span dir="ltr"><<a rel="nofollow" href="http://mc/compose?to=samikbhat@yahoo.co.in" target="_blank">samikbhat@yahoo.co.in</a>></span> wrote:<br>
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<div class="im">
hi<br>i am new to Gromacs. i want to simulate a protein inside a lipid box(preferably POPC or POPE). i have generated the protein inside the POPC box complex. But whenever i am going to build the .gro and .top file of that complex with pdb2gmx an error is creeping in saying "Cant find POP in residue topology database". it cant recognise the lipid.itp and popc.itp files which i've already put into the top directory.<br>
plese help me out.<br></div>thank you<br></td></tr></tbody></table><div class="im"><div><br>
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