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<body>#2<br>
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Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC?<br>
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Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="gmail_quote">Shima Arasteh <shima_arasteh2001@yahoo.com> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Dear gmx users,</div><div>I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file .<br></div><div><br></div><div>The .top file contains these:</div><div><br></div><div><br>[ moleculetype ]<br>; Name nrexcl<br>POPC 3</div><div>.</div><div>.</div><div>.</div><div>.<br></div><div>[ system ]<br>; name<br>POPC in water<br><br>[ molecules ]<br>; name number<br>POPC 128 <br>SOL 3800<br></div><div> <br></div><div><br></div><div>It is the command I enter:<br></div><div># make_ndx -f em.gro -o index.ndx</div><div> 0
System : 18056 atoms<br> 1 Other : 6656 atoms<br> 2 POP : 6656 atoms<br> 3 Water : 11400 atoms<br> 4 SOL : 11400 atoms<br> 5 non-Water : 6656 atoms<br><br> nr : group ! 'name' nr name 'splitch' nr Enter: list groups<br> 'a': atom & 'del'
nr 'splitres' nr 'l': list residues<br> 't': atom type | 'keep' nr 'splitat' nr 'h': help<br> 'r': residue 'res' nr 'chain' char<br> "name": group 'case': case sensitive 'q': save and quit<br> 'ri': residue index <br></div><div><br></div><div>Now, what is the correct answer? Anybody can suggest me? <br></div><div><br></div><div>Thanks in advance,</div><div>Shima<br></div><div>ge<br></div></div></blockquote></div></body></html>