Re: [AMBER] Amber_Cpptraj

From: Daniel Roe <>
Date: Fri, 13 Sep 2019 12:26:42 -0400


The question you have is pretty broad. "Changing" can mean a lot of
things. You may want to explore using the 'nativecontacts' command,
but be aware it's going to largely be up to you to define exactly what
a "hdyrophobic" contact is (typically some interaction defined by a
distance cutoff between non-polar residues).


On Tue, Sep 10, 2019 at 12:13 PM Avirup Ghosh <> wrote:
> I wanted to find how the hydrophobic and hydrophilic residues are changing
> in 300 frames of MD simulation. I tried to find similar things in Amber18
> manual but I couldn't find it. Also gave it a try in AMBERMD.ORG, but I am
> still confused. Any suggestions from your side will be appreciated.
> Thanking you,
> Avirup
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Received on Fri Sep 13 2019 - 09:30:03 PDT
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