> I have a trajectory of complex. I would like to separate the receptor and
> ligand from this. How to do this.
I would use ptraj; let's assume you have receptor as residues 1-100 and
ligand as residues 101-104. Create two ptraj scripts:
trajin mdcrd
trajout traj.receptor nobox
strip :101-9999999
avg avg-receptor.pdb pdb
Script 2:
trajin mdcrd
trajout traj.ligand nobox
strip :1-100,105-9999999
avg avg-ligand.pdb pdb
>From the average PDB files, now create two new prmtop files for the
receptor and ligand alone, in vacuo; these will be necessary to
interpret/read the new trajectory files.
--tec3
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Received on Sun Jun 22 2008 - 06:07:56 PDT
