I made a membrane in charmm gui...I didnt pay attention to water box...I did the md run in gromacs .now I want to load poly arginine peptide above the membrane by VMD but i understood that by 2.5nm distance between the peptide and membrane, peptide is out of the water box... is there any solution for me to fix it or i have to start it again by a protein/membrane system?i have to load 4 peptides above the membrane,
any suggestions??
thanks
Well, starting over with CHARMM-GUI is probably easier but you could do this.
1) Delete the waters and ions from the *.gro file.
2) Use gmx insert-molecules to place 4 peptides above the membrane.
- To do this you'd need to also make a positions.dat file that says where you want the peptides which'll look something like the one I attached.
- It'd look something like "gmx insert-molecules -f membrane_nowater.gro -ci poly_R.pdb -nmol 4 -ip positions.dat -dr 2 2 0 -o membrane_protein.gro
3) Use gmx solvate to resolvate the system.
4) Use gmx genion to add ions at your desired concentration and to potentially neutralize the system now that poly-R peptides have changed the system's net charge.
5) Throughout this you'd have to also be manually updating these changes in your topol.top topology file.
Dear JD Tamucci,
thanks for your answer
How did you make the dat file? did you calculate the numbers by any programs? is it different with posre.itp?
what about -dr? how can I specify that? and about the distance of peptides and membrane.. any commands for that?
For the positions.dat file, I just used touch positions.dat to make a text file and then edited it using vi. Yours would only have four rows of xyz coords cause you only want to place four peptides. Then I'd just choose a distance away from the membrane's headgroups I wanted the peptides to be.
The -dr flag is the allowable displacement from the xyz coords in the positions.dat file. So I set the xy coords to the xy center of my box and the z coords to my desired distance from the membrane. Then I'd probably make the -dr for x and y a little under half the respective width and length of the box and keep the z displacement at zero.
There are definitely ways to find the average z coords of the upper/lower leaflet's headgroups (e.g. gmx select, mdtraj) but you could also just look at the headgroup's z coords in the pdb or view the system in VMD and measure the distance from the bottom of the box to the headgroups.
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