AMBER Archive (2007)

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

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Apr 24 2007 - 03:30:40 CDT

Dear Jenk,

VMD can to do that fairly easy with a bit of tcl writing (which should
be very easy if you read a bit the VMD manual). Maybe you want to take a
look at it ...

or in ptraj you could in principle use the negation "~" in the mask and
"strip" everything but your desired residues .... In my understanding,
you dont need any special script to do that ...

Good luck
vlad

Cenk Andac wrote:

> 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,
>
> Jenk
>
>
>
>
>
> */Melinda Layten <mlayten_at_gmail.com>/* 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* <cenk_andac_at_yahoo.com
> <mailto: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.
>
>
>
>
>
> ------------------------------------------------------------------------
> Ahhh...imagining that irresistible "new car" smell?
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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
> E-Mail:cenk_andac_at_yahoo.com
> *
>
> ------------------------------------------------------------------------
> Ahhh...imagining that irresistible "new car" smell?
> Check out new cars at Yahoo! Autos.
> <http://us.rd.yahoo.com/evt=48245/*http://autos.yahoo.com/new_cars.html;_ylc=X3oDMTE1YW1jcXJ2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDbmV3LWNhcnM-> 

-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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