Hello justin 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
my topology file like this which I have made- topology for 1 protein molecule in 128 dmpc lipids, water and 1 counter ion. ; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with pdb2gmx, starting ; with a pdb file of tap transporter. ; make sure lipid.itp,dmpc.itp and rr1.itp are in a location where ; grompp can find them (GMXLIB, current directory, or directory given in ; the .mdp file with the include option. ; Include forcefield parameters #include "ffgmx.itp" #include "lipid.itp" #include "dmpc.itp" ; Include chain topologies #include "rr1_A.itp" #include "rr1_B.itp" ; Include position restrain protein ;#ifdef POSRES_PROTEIN ;#include "posre_A.itp" ;#include "posre_B.itp" ;#endif ; Include position restrain lipid ;#ifdef POSRES_LIPID ;#include "lip_posre.itp ;#endif ; Include water topology #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif #ifdef POSRES_WATER ;Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name PROTEIN IN DMPC BILAYER + WATER [ molecules ] ; compound #mols Protein_A 1 Protein_B 1 DMPC 128 SOL 3552 Na 1 *and the error I am getting like this- processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 1369 of the 2211 non-bonded parameter combinations ------------------------------------------------------- Program grompp, VERSION 4.0.3 Source code file: toppush.c, line: 947 Fatal error: Atomtype opls_287 not found ------------------------------------------------------- can u please suggest me is their any error in topology file and where should I have to make chnge. If I want to use ffgmx force field. as like if I want to use oplsaa force field I have to make change in lipid.itp. please suggest me what should I have to do if I am using ffgmx force field. Thanks a lot in advance.
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