Hello justin <br><br>thanks for ur suggestion . I am trying to do membrane protein simulation with lipid bilayer . I have pdb file of inserted protein in dmpc lipid bilayer. But I am facing problem in making topology file for this system.As u told in previous mail you can't combine OPLS_AA with a standerd berger lipid parameter right but even if I used the force field ffgmx than also I am getting error <br>
<br>my topology file like this which I have made-<br><br><br>topology for 1 protein molecule in 128 dmpc lipids, water and 1 counter ion.<br>; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with pdb2gmx, <br>
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 forcefield parameters <br>#include "ffgmx.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>; Include position restrain protein<br>;#ifdef POSRES_PROTEIN<br>;#include "posre_A.itp"<br>;#include "posre_B.itp"<br>;#endif<br>; Include position restrain lipid<br>;#ifdef POSRES_LIPID<br>;#include "lip_posre.itp<br>
;#endif<br><br>; Include water topology<br>#ifdef FLEX_SPC<br>#include "flexspc.itp"<br>#else<br>#include "spc.itp"<br>#endif<br><br>#ifdef POSRES_WATER<br>;Position restraint for each water oxygen<br>
[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<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 3552<br>Na 1<br><br>*and the error I am getting like this-<br><br>processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>Generated 1369 of the 2211 non-bonded parameter combinations<br>
<br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.3<br>Source code file: toppush.c, line: 947<br><br>Fatal error:<br>Atomtype opls_287 not found<br>-------------------------------------------------------<br>
can u please suggest me is their any error in topology file and where should I have to make chnge.<br>If I want to use ffgmx force field.<br>as like if I want to use oplsaa force field I have to make change in lipid.itp.<br>
<br><br>please suggest me what should I have to do if I am using ffgmx force field.<br><br><br>Thanks a lot in advance.<br><br><br><br><br>