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.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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Received on Sun Jul 09 2006 - 06:07:15 PDT
