AMBER Archive (2009)

Subject: Re: [AMBER] continuam water

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 24 2009 - 08:36:15 CDT

you might try converting the prmtop/crd to a pdb using ambpdb, and then
using a file editor like vi to delete most waters, keeping the number that
matches your trajectory file. read that into leap and don't add more water,
and you can use this new prmtop to read your trajectory of course this only
works if your trajectory has the same # of water in each frame- you didn't
say how you made it.

On Tue, Mar 24, 2009 at 12:11 AM, Mannan <malie_03_at_yahoo.co.in> wrote:

> Hi Amber users,
> I would like to check the continuam water or residence time of water in
> simulation of protein with ligand in explicit water TIP3P.
> If I keep all the water moelcules, then the trajectory becomes much larger
> for the VMD to visualise. If I remove some water moelcules, the top and crd
> files not matching.
>
> Any help is much appreciated
>
> Mannan
>
>
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