AMBER Archive (2006)

Subject: Re: AMBER: change mdcrd file to pdb file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Sep 17 2006 - 10:30:02 CDT

You are right. However, your command can only give
the last coordinates. As for the molecule is moving,
the last coordinates doe not necessarily represent a
typical coordinates. One way is to use average
structure, but some references says the final
structure needs to be energy minimized. The other way
is to use VMD to analysis the trajectory file, which
can show structure change during a time period as a
movie.

Somebody tells me Ptraj can be used to convert mdcrd
file to a series of RMSD file. But I have not tried
yet. If you know the exact command, please let me
know.

Best regards.

Fenghui Fan

--- Jianhui <tianj_at_rpi.edu> wrote:

> Hello Fenghui,
>
> Why don't you want to change mdcrd file to pdb file?
> What I know is you can change rst file to pdb file
> by ambpdb:
> $AMBERHOME/exe/ambpdb -p prmtop < rst > pdb
>
> Best regards,
>
> ======= At 2006-09-17, 01:02:54 you wrote: =======
>
> >Will you please tell me the exact command to
> convert
> >mdcrd file to pdb file by ambpdb?
> >
> >Best regards.
> >
> >Fenghui Fan
> >
> >__________________________________________________
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> Jianhui
> tianj_at_rpi.edu
> 2006-09-17
>
>
>
>
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