AMBER Archive (2006)

Subject: Re: AMBER: from traj to crd

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Tue Aug 01 2006 - 10:30:59 CDT

Hi Fabian,

Try "trajout bestC0.crd restart". By default, ptraj dumps trajectories.
To dump inpcrd format, use restart. It's described in amber manual,
ptraj section.

Guanglei

Fabián Alejandro Rodríguez wrote:
> hello,
> I ran MD and I have a snapshot of the trajectory that I want to take out
> and minimise energy.
> I can extract the coordinates, but probably in the wrong format to be
> read by sander. I did
> trajin ../iBdnaVac300KequilEnd200psC0.traj 15 15
> trajout bestC0.crd
>
> and this crd file is different from the inpcrd that I had for the fist
> time from tleap.
>
> the question is: How do I extract the coordinates from the trajectory in
> the right format to then minimise energy?
>
> thank you,
> fabian.
>
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