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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--
========================================
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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