<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi all,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I had similar problem with Fatal errors with Atomtype LC3 not found while setting up a POPC simulation. After a day of trying out different things I figured out the problem. And I would like to share my experience in the mailing list. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Renaming of POP to POPC in the .gro files doesn't matter... the main thing is to change the [Defaults] in the lipid.itp file (this eliminates the LC3 atomtype not found error)</DIV><DIV>my .top files and modified lipid.itp files look like.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>---------------------------------------------------</DIV><DIV>grompp.top</DIV><DIV>--------------</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>#include "ffgmx.itp"</DIV><DIV>#include "lipid.itp"</DIV><DIV>#include "popc.itp"</DIV><DIV>#include "protein.top"</DIV><DIV>#include "spin.top"</DIV><DIV>#include "ions.itp"</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>#ifdef FLEX_SPC<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>; removed these following lines from the protein.top file and appended into one single .top file.</DIV><DIV>#include "flexspc.itp"</DIV><DIV>#else</DIV><DIV>#include "spc.itp"</DIV><DIV>#endif</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>#ifdef POSRES_WATER</DIV><DIV>; Position restraint for each water oxygen</DIV><DIV>[ position_restraints ]</DIV><DIV>; i funct fcx fcy fcz</DIV><DIV> 1 1 1000 1000 1000</DIV><DIV>#endif</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>[ system ]</DIV><DIV>; name</DIV><DIV>BR_103C</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>[ molecules ]</DIV><DIV>; name<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>number</DIV><DIV>Protein <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>1</DIV><DIV>DRG<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>1</DIV><DIV>POPC<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>154</DIV><DIV>SOL <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>13393</DIV><DIV>---------------------------------------------------</DIV><DIV><SPAN class="Apple-style-span">lipid.itp <FONT class="Apple-style-span" color="#FF0C00">(notice the defaults directive is commented out... this eliminates the AtomType 'LC3' not found error)</FONT></SPAN></DIV><DIV>---------</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS</DIV><DIV>;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et</DIV><DIV>;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are</DIV><DIV>;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,</DIV><DIV>;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as</DIV><DIV>;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><FONT class="Apple-style-span" color="#FF1500">;[ defaults ]</FONT></DIV><DIV><FONT class="Apple-style-span" color="#FF1500">;1 1</FONT></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>[ atomtypes ]</DIV><DIV>;name mass charge ptype c6 c12</DIV><DIV>;</DIV><DIV> LO 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS</DIV><DIV> LOM 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS</DIV><DIV> LNL 14.0067 0.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS</DIV><DIV> LC 12.0110 0.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS</DIV><DIV> LH1 13.0190 0.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS</DIV><DIV> LH2 14.0270 0.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS</DIV><DIV> LP 30.9738 0.000 A 9.16000e-03 2.50700e-05 ;phosphor, OPLS</DIV><DIV> LOS 15.9994 0.000 A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS</DIV><DIV> LP2 14.0270 0.000 A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ</DIV><DIV> LP3 15.0350 0.000 A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ</DIV><DIV> LC3 15.0350 0.000 A 9.35700e-03 3.60900e-05 ;CH3, OPLS</DIV><DIV> LC2 14.0270 0.000 A 5.94700e-03 1.79000e-05 ;CH2, OPLS</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>contd...............</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>---------------------------------------------------</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>That is all the modifications required for running the simulation. Hope this helps people with similar problem in the future.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Venks</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>Venky Krishnamani</DIV><DIV>Dr.Janos K. Lanyi Lab,</DIV><DIV>D320, Medical Sciences D</DIV><DIV>University of California, Irvine</DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR><DIV><DIV>On May 29, 2006, at 12:23 PM, Arindam Ganguly wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi All,<BR>thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.<BR>Arindam Ganguly <BR><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>