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

From: Cenk Andac <>
Date: Mon, 23 Apr 2007 15:35:36 -0700 (PDT)

Hi Melinda,

Thanks for replying. I have a ligand bound to a macro molecule with two water molecules forming hydrogen bonding bridges at two different loci between the binding site and two different nitrogen rich groups of the ligand. I would like to extract coordinates from a trajectory for the ligand part of a complex including two water molecules that make hydrogen bonding interactions with those nitrogen rich groups of the ligand.

Your assistance for providing me with such a useful script to meet the criteria mentioned above would be greatly acknowledged.

my best regards,


Melinda Layten <> wrote: 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 <> 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,


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,



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   Cenk Andac, M.S., Ph.D. Student
 School of Pharmacy at
 Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
 Etiler, Ankara, 06330 Turkey
 Cell: +90-(536)-4813012

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Received on Wed Apr 25 2007 - 06:07:25 PDT
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