[gmx-users] Add ligand molecules in a lipid bilayer

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 27 13:02:02 CET 2011

On 27/11/2011 7:23 PM, parto haghighi wrote:
> Dear gmx_users,
> I am working on lipid/drug molecule system.
> I could make the ligand topology by PRODRG and get DMPC.itp from 
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies.
> To add ligand molecule I first changed its coordinate by:
> editconf -f drg.gro -o drg_newbox.gro -c -box  6.17600   6.17600   5.50000
> then add drg_newbox.gro to my bilayer by:
> cat drg_newbox.gro dmpc_whole.gro > system.gro

Updating the number of atoms and shifting the box line, of course...

> How can I add 6 ligand molecules in lipid bilayer symmetrically at 
> each side of membrane?

Suitable use of editconf options to do translations, or maybe genconf 
can achieve this.

> What is gromacs command to add molecules in bilayer (except editconf)?

There is none.


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