AMBER Archive (2009)

Subject: Re: [AMBER] How to delete the frames at specific intervals

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Fri Apr 03 2009 - 04:55:35 CDT

Hi,
You can process your trajectory with ptraj to output every 5th frame in a
new trajectory and then load it in vmd.
trajin name.crd 1 5000 5
trajout new.crd

Every 5th frame will be written in new.crd.

Bala

On Fri, Apr 3, 2009 at 3:16 AM, Mannan <malie_03_at_yahoo.co.in> wrote:

> I have a trajectory of 5ns with frames from each pico seconds and water
> molecues around the protein 8A. When I load in VMD my system could not
> handel its memory.
> I would like to delete the frmes with 5ps interval using ptraj.
>
> I could not do that. Please help me out.
> Thanks in advance
> Thomas
>
> --- On Thu, 2/4/09, David A. Case <case_at_biomaps.rutgers.edu> wrote:
>
>
> From: David A. Case <case_at_biomaps.rutgers.edu>
> Subject: Re: [AMBER] please help me out
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Thursday, 2 April, 2009, 11:18 PM
>
>
> On Thu, Apr 02, 2009, bharat lakhani wrote:
>
> > here i am sending my drug file.i want to do minimization.Could anyone
> please
> > let me know.what would be the *minvac.in file for this antibiotic.*
>
> Sounds like you should follow Tutorial B4, at
> http://ambermd.org/tutorials.
>
> ...dac
>
>
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