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.
-Justin
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.
thanks.
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
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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