[gmx-users] grompp error in running simultion of membrane protein with lipid bilayer
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 3 12:30:01 CEST 2009
nitu sharma wrote:
> Dear all,
> I am trying to do simulation of membrane protein with
> lipid bilayer for this I have made topology file like this-
> ; topology for tap in 128 dmpc lipids plus water.
> ; 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 "ffoplsaa.itp"
> #include "lipid.itp"
> #include "dmpc.itp"
This will not work. I said the exact same thing to someone else not two or
three days ago. You cannot combine OPLS-AA with the standard Berger lipid
parameters; the Berger atom types are for use with a Gromos force field.
You have three options:
1. Use a Gromos force field variant. You still can't simply #include
"lipid.itp," however, you will have to append the relevant directives to the
ff*nb.itp and ff*bon.itp and use these modified files.
2. Modify lipid.itp to be in accordance with OPLS-AA conventions. Chris Neale
has posted a detailed procedure to do this; search the list archive.
3. Use the self-consistent Gromos96 53a6 force field parameters that have been
uploaded to the Users' Contributions section of the website.
The choice is up to you, based on which setup you think is best for your system.
> when I am trying to run grompp after solvating the system I am getting
> error like this-
> Program grompp, VERSION 4.0.3
> Source code file: toppush.c, line: 843
> Fatal error:
> Atomtype C not found
Right, do you see atomtype "C" anywhere in ffoplsaa.atp? This atomtype belongs
to a Gromos force field.
> my command line like this-
> grompp -f em.mdp -p rr1-dmpc.top -c solvated-tapp-mod.pdb -o tapp-mod-em.tpr
> if anyone know about this please suggest me right thing to do.
> Nitu Sharma
> School of life sciences
> Jawaherlal Nehru University
> New Delhi India
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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