[gmx-users] Membrane protein simulation

Behnoush Zare bzare at iums.ac.ir
Wed Dec 19 10:23:52 CET 2007

Dear Yanzi,
Forthunatly my simulation was run. this time I select the pope files of the Dr Tieleman's site and create the protein_in_pope.pdb with ffgmx force field.
Then I ran genbox to solvate the system and delete some pope which had crash with the protein.Also I added #include "lipid.itp" in the last generated .top file and change the charactr of system at the end of the file based on the total number of protein.pope and water. So grompp has been run.
But I have already two questions. After grompp, I ran genion to neutralize the system. But this run has not any output and it seems it has stopped in this step by these two lines in the end:

Number of (3-atomic) solvent molecules: 6113
Replacing solvent molecule 717 (atom 18791) with CL- 

and there is no interaction. Could you please explain to me what it means and what I should do.
Another problem is the protein size is greater than the box in the both sides. What is your suggestion to me for expanding the water size in both sides of the box?
Thank you very much in advance for your very kind help.

Best regards

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