AMBER Archive (2009)

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

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Wed Jul 08 2009 - 10:01:27 CDT

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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