I have lipid bilayer which is pack in packmol, after solvation in GROMACS, I don't want the water molecule in the lipid tail region for MD simulation. So can anyone help me to remove the water molecules from core of bilayer.
This could be the rough procedure:
Create the index file containing your tails (TAILS.NDX) with gmx_make_ndx, and then:
#creating new index file for atoms to keep from your structure (SOLVATED.pdb):
gmx select -s SOLVATED.pdb -n TAILS.ndx -select "not (same residue as ((within 1,0 of TAIL) and resname SOL))" -on atoms-to-keep.ndx
#Write out the kept atoms:
gmx editconf -n atoms-to-keep.ndx -f SOLVATED.pdb -o bilayer+kept_water.pdb
There is a water_deletor.pl script available to download in the membrane protein (KALP) simulation tutorial with GROMACS, and instructions on how to use it.
http://www.mdtutorials.com/gmx/membrane_protein/03_solvate.html
Miloš T. Ivanović
I have attached the image of bilayer which is solvated in GROMACS
According to your answer i made the index file for HEAD, because I have to remove water molecule from whole bilayer HEAD to HEAD of lipid. But I'm getting the error it shows that;
Error in user input:
Invalid command-line options
In command-line option -select
Invalid selection 'not(54ZX(80,0 of HEAD) and resname SOL))'
Near '54ZX'
syntax error
I'm not getting whether I'm not selecting proper region or in command line option -select not putting the in the proper way.
Please could you little elaborate it. I have to remove water molecule from 4.0 nm to 12.0 nm, this is the HEAD to HEAD distance along z direction. Then how can be select. 54ZX is the resname for lipid.
Thank you
Wojciech Kopec
Just as you mention I have followed all the steps but unfortunately, Im not able to save the files together. Can you please help me with this
Nandan Kumar
and Dheeraj PrakaashI had download the perl script from KALP simulation, but it remove counted number of water molecules. Actually in my case I want to remove those water molecule which are in between the bilayer from head to head region. It will become very challenging to remove the water molecule manually. I have attached the image of bilayer with water for your reference.
Thank you
You can also open your PDB file in Chimera and delete the waters by selecting a rectangular space. If you are ok with sharing your PDB file, I can do that for you quickly. DM me.
Nandan Kumar
, Anjana's lipids are called 54ZX. I don't know what those are. From the picture, they don't look like any kind of lipid that I've seen available on CHARMM GUI. Manual removal of water is probably a better option in this scenario. I would recommend using PyMOL or Chimera for the user-friendliness. VMD may not be as straight-forward if Anjana has not used it before.
Dheeraj Prakaash and Nandan Kumar
, 54ZX is the residue name of lipid which is here used and it is not available on CHARMM-GUI.
Wojciech Kopec
, I could save it as told by you, but i could not remove water molecule completely. H2O (all three atoms) is not getting remove, sometimes only two or one atom is remove from water. I'm getting error that number of coordinates in coordinate file (bilayer_water.gro) does not match topology, as water is getting remove partially. I cannot remove it manually as total number of water molecule is > 50000. Can you help me
Hi Anjana. In response to your question to Wojciech Kopec
, there is a way to select whole water molecules in VMD which are within a certain cutoff.To select just atoms within a cutoff, your VMD selection will look something like this (just an example):
resname SOL and (z>100 or z100 or z
You can always ask your GROMACS-related questions (only) on the GROMACS forum and get an answer directly from gmx experts:
https://gromacs.bioexcel.eu/
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