Dear all,<br><br> I am trying to do simulation of membrane protein with lipid bilayer for this I have made topology file like this-<br>; topology for tap in 128 dmpc lipids plus water.<br>; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with pdb2gmx, starting<br>
; with a pdb file of tap transporter.<br>; make sure lipid.itp,dmpc.itp and rr1.itp are in a location where<br>; grompp can find them (GMXLIB, current directory, or directory given in <br>; the .mdp file with the include option. <br>
#include "ffoplsaa.itp"<br>#include "lipid.itp"<br>#include "dmpc.itp"<br><br>; Include chain topologies<br>#include "rr1_A.itp"<br>#include "rr1_B.itp"<br><br>;#ifdef POSRES<br>
;#include "posre_A.itp"<br>;#include "posre_B.itp"<br>;#include "lipid_posre.itp"<br>; Include water topology<br>#ifdef FLEX_SPC<br>#include "flexspc.itp"<br>#else<br>#include "spc.itp"<br>
#endif<br><br>[ system ]<br>; Name<br>PROTEIN IN DMPC BILAYER + WATER <br><br>[ molecules ]<br>; compound #mols<br>Protein_A 1<br>Protein_B 1<br>DMPC 128<br>;SOL 3551<br><br>SOL 24020<br>SOL 43676<br>
<br>when I am trying to run grompp after solvating the system I am getting error like this-<br>Program grompp, VERSION 4.0.3<br>Source code file: toppush.c, line: 843<br><br>Fatal error:<br>Atomtype C not found<br>--------------------------<br>
my command line like this-<br>grompp -f em.mdp -p rr1-dmpc.top -c solvated-tapp-mod.pdb -o tapp-mod-em.tpr<br> if anyone know about this please suggest me right thing to do.<br>thanks.<br><br>Nitu Sharma<br>School of life sciences<br>
Jawaherlal Nehru University<br>New Delhi India<br><br><br>