AMBER Archive (2008)

Subject: Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Fri Nov 07 2008 - 10:24:03 CST

>
>
> PPS, thinking about this some more, your answer would seem to imply
> that the identities of the waters selected by distance would be fixed
> by the reference coordinates. That does not work very well for my
> purpose, since I wanted to see the waters come and go into and out of
> the region of the active site over the trajectory. Is this correct?
>

Yes, the identities of water molecules will be fixed throughout the entire
trajectory. With the distance criteria, the number of water molecules may be
different for each frame. You can try the "closest" command in ptraj to
retain a fixed number of closest water molecules.

Jianyin

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