Dear Yanzi,
Thank you for your swift response. I did all you wrote to me. Also I include
ffG43a1 forcefield in the lipid.itp file and then include the lipid.itp file in
the protein.top at line 12 as forcefield parameter. When I run grompp the
following error appeared:
Fatal erroe; Invalid order for directive moleculetype, file "protein.top",
line 14
What is this error and what do I have to do?
Thank you in advance for your valuable aid.
Best regards,
Behnoush Zare
Iran University of Medical Sciences,
Department of Pharmacology
-----------------------------------------------------------
Dear Yanzi zhou,
I am a new gromacs user and reading your message sent by gmx-users in my mail
box I found that you have worked on lipid bilayer simulation. My outlook
express is out of work so I had to mail to you directly.
Sorry about I don’t have any response to your question my problem is a
protein-lipid bilayer simulation.
I am trying to perform MD Simulation on a membrane protein within the lipid
bilayer, popc. I have the .pdb and the .top file of the protein. Also I have
got the popc.pdb, popc.itp and lipid.itp files from the site of Dr. Tieleman at
the Calgary University. I have visited the www.wiki.gromacs.org site,
specially the lecture of Gromacs tutorial for membrane protein simulations by
Dr. Phil Biggin, but that is not enough to running the simulation. For example
after creating the pdb file including protein and popc what is the top file to
running grompp.
Would you please kindly provide me the step by step method for performing MD
Simulation on a protein within lipid bilayer.
Thank you in advance for your valuable help. I am looking forward to
hearing from you.
Best regards,
Behnoush Zare
Iran University of Medical Sciences,
Department of Pharmacology
Hello, Behnoush:
I'm glad to help you though I'm a green hand myself.
You should create the topology file for lipids by yourself.
For example, if you do simulation for lipids only, first, copy lipid.itp
and popc.itp to the ~/GROMACS/share/top/, then if you have included
other force field in your top file, such as ffgmx.itp, open lipid.itp,
delete the two lines:
[ defaults ]
1 1
and then prepare the top file for lipids by yourself. Following is an
example for POPE:
;
;
; Include forcefield parameters
# include "ffgmx.itp"
# include "lipid.itp"
; Include water topology
#include "spc.itp"
; Include topology for lipids
#include "pope.itp"
[ system ]
; Name
POPE in water
[ molecules ]
; Compound #mols
POPE 340
SOL 6729
If you do simulation for lipids and protein, first, you can create the
top file for protein using pdb2gmx, then in the top file, you may add
such lines at the bottom:
; Include topology for lipids
#include "pope.itp"
[ system ]
; Name
Protein in POPE
[ molecules ]
; Compound #mols
Protein 1
POPE 340
SOL 6729
Best wishes.
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