AMBER Archive (2009)

Subject: [AMBER] How to remove Hydrogen using ptraj

From: Mannan (malie_03_at_yahoo.co.in)
Date: Tue Sep 01 2009 - 05:50:44 CDT

Hi,
 
I would like to remove hydrogen from the trajectory before converting into PDB.
But I could not remove hydrogen using strip :H or strip :H*
When using strip :H
none of the hydrogen where removed
when using strip :H*
only 34 not all the hydrogen were removed.
 
 
How to remove all the hydrogen using ptraj.
 
Thanks,
Mannan

--- On Mon, 31/8/09, Mannan <malie_03_at_yahoo.co.in> wrote:

From: Mannan <malie_03_at_yahoo.co.in>
Subject: [AMBER] Query regarding watershell command
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Monday, 31 August, 2009, 4:08 PM

Hi AMBER people,
 
I have used WATERSHELL in ptraj for set of trj files.
 
In the first frame I got number of water molecules as 400 for a distance cutoff  of 3.5 A for any atoms.
But when I see in VMD I could see only 5 water molecules within 3.5 for a set of residues.
How come this big difference. Do i miss anything.
 
Is that possible to writeout pdb with water molecules within 3.5 for a set of residues from traj.
 
Mannan

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