AMBER Archive (2007)

Subject: Re: AMBER: extracting coordinate from crd file

From: Amit Kumar (amitkumar346_at_gmail.com)
Date: Sat Feb 10 2007 - 09:31:35 CST

Hi Gurpreet,

ambpdb - convert amber-format coordinate files to pdb format.

*ambpdb* is a filter to take a coordinate "restart" file from an AMBER
dynamics or minimization run (on STDIN) and prepare a pdb-format file (on
STDOUT). The program assumes that a *prmtop* file is available, from which
it gets atom and residue names.

I hope it helps.

Amit

On 2/10/07, gurpreet singh <gps.iitm_at_gmail.com> wrote:
>
> Dear Mr.Ilyas and Amber users,
>
> Thank you so much for your kind reply Mr. Ilyas.
>
> But I want to know one thing, My Amber version is 9 and When I went
> through the forum I found that there is one module called CARNAL and with
> that it seems that we can extract the coordinates of a particular amino acid
> over a period of time from the trajectory. I don't know whether I have that
> option in my Amber version or not. If not is there any other option to do
> this? It would be of great help to me if some of you could help me in this
> problem.
> Many thanks in advance.
>
> With regards,
> Gurpreet Singh, M.S,
> Department of Biotechnology,
> Indian Institute of Technology, Chennai,
> Chennai - 36.
> +91 - 9357377477
>
>
>

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