Hi everyone,
I am using vmd to create input files for my system. I have protein-membrane system, in which protein is partially solvated in water. I intend to fully solvate the protein and generate the input file.
I tried command
package require psfgen
solvate system_latest_autopsf moved.pdb -b 2.4 +z 5 -z 5 -o solvated
It works well for Z axis but it also puts water on to x-y direction. I intend to get a continuous bilayer (with periodic boundary conditions) on the x-y plane. Any idea how can I achieve that ?
I am attaching some necessary files and snapshots.
Thanks,
Vikas
Hi, if you are using gromacs (it should also work on others but in gromacs it is tested), first change the box size on x, y to be at max the size of the lipid bilayer. Then solvate your system. This won't add water mols on the unnecessary areas. There is also this script:
Our script is set to select the Z axis. If you want to get the Y axis, just change the $(NF) value to $(NF-1) and $(NF-4) in lines 12 and 23, respectively. Same idea to X axis (changing to 2 and 5). The editable variables for upper and lower threshold are shown as up and down (lines 2 and 3), respectively. The script is presented below:
############
#!/bin/bash
up=5.414
down=1.788
watercount=0
read_n() { for i in $(seq 3); do read || return; echo "$REPLY"; done; }
cat $1 | grep -v 'SOL' | sed \$d >solvate_clean.gro
cat $1 | grep 'SOL' | (while lines=$(read_n); do
vel=$(echo "$lines" | head -1 | awk '{print NF}')
if [ $vel -le "6" ]; then
atom=$(echo "$lines" | grep ' OW' | awk '{print $(NF)}')
exp1=$(echo "$atom >= $up" | bc)
exp2=$(echo "$atom = $up" | bc)
exp2=$(echo "$atom
Hi Vikas
Honestly, I don;t know how to create a simulation box in VMD but can create it using GROMACS commands such as editconf, genbox. First, converted pdb file into gro file then, extended box size in Z direction. Finally, added water molecules using genbox command find attached. If it doesn't work set up larger box size. I dont know exact size of the box. Find attached.
Use VMD plugin Add solvation box and act accordingly to get desired structure
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