Hi,<br>While trying to setup a membrane inserted protein simulation I get this following error while running grompp command. <br><br>% grompp -v -f em.mdp -c br1.pdb -p example.top -o br_emin.tpr<br><br><span style="color: rgb(255, 0, 0);">
Generated 1369 of the 2211 non-bonded parameter combinations</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Excluding 3 bonded neighbours for Protein_A 1</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">Cleaning up temporary file gromppjh3WI9</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">-------------------------------------------------------</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">Program grompp, VERSION 3.3.1</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Source code file: toppush.c, line: 891</span><br style="color: rgb(255, 0, 0);">
<br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Fatal error:</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0); font-weight: bold;">moleculetype K is redefined</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">-------------------------------------------------------</span><br><br>But there are no moleculetypes K in my simulation and I have not generated any ions yet. I also had to do setup other lipids but again ended up in the same error. Please help...thanks in advance... below are the details of my input files.
<br><br>EM.mdp options<br>--------<br>title = BR_POPC<br>cpp = /usr/bin/cpp ; the c pre-processor<br>define = -DFLEXIBLE<br>constraints = none<br>integrator = cg<br>dt = 0.002 ; ps !<br>nsteps = 1000<br>nstlist = 5<br>ns_type = grid
<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff
<br>;<br>emtol = 1000.0<br>emstep = 0.01<br><br>--------------------<br>TOP File input<br>----------------<br><br><br>#include "ffgmx.itp"<br>#include "lipid.itp"<br>#include "popc.itp"<br>#include "
br.top" ;; protein topology<br>#include "ions.itp"<br><br>#ifdef FLEX_SPC<br>#include "flexspc.itp"<br>#else<br>#include "spc.itp"<br>#endif<br><br>[ system ]<br>; name<br>BR_POPC<br>
<br>[ molecules ]<br>; name number<br>Protein 1<br>POPC 56<br>SOL 4412<br>----------------------------------- <br><br clear="all"><br>-- <br>Venky Krishnamani<br>Graduate Student, <br>Dr. Janos K. Lanyi Lab<br>Univerisity of California, Irvine
<br>Irvine, CA<br>(949) 232-3021