AMBER Archive (2007)

Subject: Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2

From: Melinda Layten (mlayten_at_gmail.com)
Date: Mon Apr 23 2007 - 16:52:26 CDT

In general, it's not that hard to write a script to extract trajectory
frames that meet X criteria. We use several standard scripts here to grab
frames where a previously generated data file is within a specified
criteria, and skip frames that don't match that criteria. Ptraj is a tool,
but if you have new ideas you can't be afraid to try things on your own.

Good luck.

Melinda Layten

On 4/17/07, Cenk Andac <cenk_andac_at_yahoo.com> wrote:
>
> Hi again,
>
> This is in addition to my previous E-Mail.
> I was also wondering if the ptraj command "contacts" would meet my
> requirements .
>
> my best regards,
>
> jenk
>
>
> Dear AMBER developers,
>
> I would appreciate it very much if someone in the future add a useful
> command in ptraj that would enable me to extract only certain snapshots of a
> trajectory in which one or more water molecules (user should also have an
> option with numbers, like one to infinity would be nice !) within a
> H-bonding distance to a defined atom(s) in a binding site or on a bound
> ligand and recompile those selected snapshots into a new trajectory. This
> idea would get me a good paper I believe.
>
> best regards,
>
> Jenk.
>
>
>
>
>
>
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>

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