[gmx-users] Membrane protein simulation

[Behnoush Zare]

Dear Yanzi,Dear users,

Finally the genbox was run probably it was related to my gromacs compilation on red hat 5. But I have another question. After running simulation (the position-restrained molecular dynamics simulation) on the system including protein, pope, water and CL for 100 ps, the position of the lipid tails 
has changed that it seems the lipids of one side ward off the lipids of the other side. I think I should use a posre.itp for lipid to keep the bonds from any position changing but letting the lipid molecule to go around the protein. How can I obtain or generate this file. After all , am I right?

Happy new year,
Behnoush
----- Original Message -----
From: "Yanzi Zhou" <yz30 at nyu.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Saturday, December 22, 2007 11:37:59 PM (GMT+0330) Auto-Detected
Subject: Re: [gmx-users] Membrane protein simulation

Dear Behnoush:
> Dear Yanzi, 
> Of course the system charge is 30+ so I have to add 30 Cl- . So I put “nn 30” to the command like this: 
> genion -s protein_pope_em.tpr -o protein_pope_ion.pdb -nname CL- -nn 30 -g protein_pope.log
> But it seems only one water has been replaced with Cl-. Do I have to repeat this step for 30 times?!! or something wrong in this command. 
>   
Maybe something is wrong. Generally, you only need to do this for one 
time. The command is right. Check your pdb file. One more thing, you 
should add water first, then add ions.
> The protein is larger than box in the Z axis. I tried to add more water in the Z axis by genbox but it just added a few water in one side despite it needs more. Could you please tell me what I should do to fill the empty regions of the box with water. What do you mean about the pope may not be suitable for this protein and how do you understand it? 
>   
When adding water, before using genbox, you can use editconf at first. 
For Gromacs, The origin of a box is always at (0, 0, 0). When you modify 
the box size by genbox, the coordinates of the system wouldn't change. 
By editconf, you can center molecule in box, translate or rotate the 
molecule. When you use RASMOL to view the image, type "unitcell true", 
you can see the box. Maybe VMD has the same function, but I just don't 
know.
What membrane is the protein found from? What does the membrane consist 
of? Is the protein active in POPE? Read literature carefully, and choose 
the suitable lipids.
> Thank you very much in advance for your kindness and expertize. 
>
> Best regards, 
> Behnoush 
>
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Best regards.
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