AMBER Archive (2009)

Subject: Re: [AMBER] ouput trajectory of only CA atom

From: Jordan Monnet (monnet.jordan_at_free.fr)
Date: Wed Jul 08 2009 - 11:03:32 CDT

Hello,

Whether you need pdb files, you could do something like :

trajin ub_anal.crd

image origin
strip !@CA

trajout ub_ca.pdb pdb nobox
go

This input would give you a pdb for each step of your trajectory, you may
want to select only the step you whish.

Jordan
 
* Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de) wrote:
> Dear Bala,
>
> Yes you would need a topology file that contains only CAs. To my
> knowledge, Leap cannot do that ... It would be nice feature though ...
>
> What you can do is to create a pdb file with only the CAs and then use
> that as topology file to visualize ... At least in VMD it works .. it
> should in Pymol as well ...
>
> Vlad
>
> Bala subramanian wrote:
> >Hello,
> >
> >with just
> >
> >strip !@CA
> >
> >Ptraj works without any error. But when i make a pdb from the stripped
> >trajectory, Ptraj shows the other atoms also in the pdb file. Do i need to
> >create another prmtop consisting of only CA information to work with the
> >trajectory of only CA atoms. I do not know if it is possible to create such
> >a prmtop file for just the CA atoms. Is there any way to do the same ?
> >
> >Bala
> >
> >On Wed, Jul 8, 2009 at 4:41 PM, Carlos Simmerling <
> >carlos.simmerling_at_gmail.com> wrote:
> >
> >
> >>have you tried just
> >>strip !@CA
> >>
> >>what exactly does ptraj say it is doing with your mask? it should tell you
> >>#
> >>atoms that match, etc.
> >>
> >>On Wed, Jul 8, 2009 at 9:24 AM, Bala subramanian
> >><bala.biophysics_at_gmail.com>wrote:
> >>
> >>
> >>>Friends,
> >>>
> >>>How can i ask ptraj to output the coordinate of only the CA atoms from a
> >>>trajectory file. I tried with following input but it vain. Is there
> >>>anything
> >>>wrong with the mask.
> >>>
> >>>trajin ub_anal.crd
> >>>trajout ub_ca.crd
> >>>strip @* &! @CA
> >>>
> >>>
> >>>Thanks,
> >>>Bala
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> >>>
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> >
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533202
> 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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-- }><(({*>

Jordan MONNET
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)
Phone: +336 20 70 24 93

http://monnet.jordan.free.fr/

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