AMBER Archive (2006)

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

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Jul 06 2006 - 17:03:12 CDT

You can do the analysis using hbond which is not limited
only for H-hond or closest in ptraj.

You can do that using VMD also.

On 7/6/06, Scott Pendley <scott.pendley_at_gmail.com> wrote:
> 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
>
> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
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Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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