[gmx-users] problem in topology file for protein+lipid bilayer system

[Justin A. Lemkul]

nitu sharma wrote:
> 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.

Let me guess, you didn't re-process your protein with pdb2gmx to create a new 
topology?  The presence of "opls_XXX" is a pretty clear indication that you are 
using OPLS-AA.  You cannot magically #include some other force field and expect 
it to work.  Start over.

-Justin

> 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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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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