[gmx-users] Membrane protein MD Simulation

[Behnoush Zare]

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
 

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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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