Dear all,
We need to pack a simulation box of cubic shape with molecules A and B such that a single protein molecule A lies in the centre of the cube and ‘N’ number of B molecules around A spaced at equal distance from each other (Figure attached below for your kind reference). The coordinates of both molecule types are available in PDB format. Is there any program in GROMACS 5.1 or external tools or scripts to place the molecules orderly in a cubical box? I would be grateful for your kind suggestions or help.
Thank You
Dear Arun Bahadur Gurung,
You can use PACKMOL for building initial configuration for MD simulations by packing molecules in defined regions of space. Also, the gmx insert-molecules tool of GROMACS can be used with the "-ip" option to insert molecules only at the positions defined in the positions.dat file.
- PACKMOL package: http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml
- gmx insert-molecules tool: https://manual.gromacs.org/current/onlinehelp/gmx-insert-molecules.html
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