I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :(<br><br>This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane system ( I've tested for both cases)<br>
<br>; Include chain topologies<br>#include "charmm36.ff/forcefield.itp"<br><br>; Include lipids<br>#include "charmm36.ff/lipids.rtp"<br><br><br>; Include water topology<br>#include "/charmm36.ff/tip3p.itp"<br>
<br>; Include ion topologies<br>#include "charmm36.ff/ions.itp"<br><br>; System specifications<br>[ system ]<br>128-Lipid POPC Bilayer in water<br><br>[ molecules ]<br>POPC 72<br><br>When I've loaded my molecule to grompp I've obtained error<br>
<br>Program grompp, VERSION 4.5.4<br>Source code file: /tmp/gromacs-4.5.4/src/kernel/toppush.c, line: 770<br><br>Fatal error:<br>Unknown bond_atomtype 1<br><br>What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ?<br>
<br><br>James<br><br><div class="gmail_quote">2011/10/20 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear, Gromac's users!<br><br><br>Today I've tried to make pure lipid bi-layer system from initial .pdb structure with the parametrization by the charmm ff. The main goal of this step is preparing the initial structure suitable for the futher simulation ( creating gro, top and posre files)<br>
<br>First I've download s system consisted of 72 dppc lipids solved with water. Then I've succesfull created .gro as well as .top files by the pdb2grmx for my lipid system.<br>But on futher during creatinon of the tpr file by gromp I've obtained many errors like this<br>
<br><br>ERROR 4378 [file topol.top, line 83773]:<br> No default U-B types<br><br>Also I've tried to make my own bi-layer by VMD membrane plugin. After processing of this file by pdb2gmx I've obtained many .itp files like topol_Other_chain_L2.itp included in the generated topology file topol.top.<br>
<br>But during loading this structure to the grompp I've obtained above mentioned error again. In both cases I've used mdp file for gromp consist of minimization algorithm ( attached).<br><br>What I've done wrong? Could you provide me with the workable algorithm for preparation of the pure lipid system parametriezed by charm27 ?<br>
<br><br>Finally I have small queation about charmm structures- I've found already pre-equilibrated bi-layers <a href="http://terpconnect.umd.edu/%7Ejbklauda/research/download.html" target="_blank">http://terpconnect.umd.edu/~jbklauda/research/download.html</a> where each pdb file is accompanied by the PSF ones. As I've understood the PSF is the same to the top in the Gromacs. Could I convert PSF to the TOP for already pre-built system?<br>
<br><br>Thanks for help<br><br>James<br><font color="#888888"><br>James<br>
</font></blockquote></div><br>