AMBER Archive (2006)

Subject: Re: AMBER: analysis of ATOMs in ´certain range distance during simulation

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Thu Jul 06 2006 - 16:47:57 CDT

I am not sure if this will help but have you considered using a
visualization program like VMD or Swiss PDB viewer.

On 7/5/06, pkb bioinfo <pkstruct_at_gmail.com> wrote:
>
> Dear Amber users,
>
> I am a new AMBER user and finding it very difficult to analyse my
> simulation result.
> I need to know atoms in a range (4A) of a certain residue of importance
> during
> simulation.Actually I want to know which residues or atoms come close to
> my docked
> substate during course of simulation.
>
> I saw in the carnal it was possible but carnal module is not present in
> AMBER8.
> In ptraj hbond analysis it will give only potential hydrogen bonds.
> So anyone please help me in this regard.
>
> best regards
> Pravas
>

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