AMBER Archive (2008)

Subject: Re: AMBER: trajout input

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri Jun 20 2008 - 12:57:43 CDT

> 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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