AMBER Archive (2009)

Subject: Re: [AMBER] using ptraj

From: Molecular Dynamics (amberquestion_at_yahoo.com)
Date: Tue Feb 17 2009 - 07:31:02 CST

[root_at_fencevrepc-84-23 deneme]# ptraj foo.prmtop < trajin.in

  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 9.0 integrated" (April 2006)
  -/- Executable is: "ptraj"
  /-\
  \-/ Residue labels:

TES TES TES TES TES TES TES TES TES TES
 ...

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin equ.mdvel 200 200 1
  Checking coordinates: equ.mdvel
FYI ptrajSetupIO(): trajin stop value (200) is greater than the number of sets read in.
Setting stop to the maximum value (20)
WARNING in ptrajSetupIO(): trajectory start is > stop; no
configurations will be processed

PTRAJ: trajout velocity.rst restart

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on -342 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (equ.mdvel) is an AMBER trajectory with 20 sets (processing only -342)

OUTPUT COORDINATE FILE
  File (velocity.rst) is an AMBER restart file with box information

NO ACTIONS WERE SPECIFIED

Processing AMBER trajectory file equ.mdvel

Set 1

PTRAJ: Successfully read in 20 sets and processed 0 sets.
       Dumping accumulated results (if any)

________________________________
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Tuesday, February 17, 2009 2:37:15 PM
Subject: Re: [AMBER] using ptraj

what did ptraj say it was doing in the output?

On Tue, Feb 17, 2009 at 6:44 AM, Molecular Dynamics
<amberquestion_at_yahoo.com> wrote:
> Dear Carlos,
>
> I did the same proccess with the mdvel file, but ptraj didn't extract the snapshot that is the same with my foo.rst file. My ptraj input files are
>
> trajin equ.mdcrd 200 200 1 ( It worked fine )
> trajout foo.rst restart
>
> trajin equ.mdvel 200 200 1 ( I didn't get velocity.rst file )
> trajout velocity.rst restart
>
> What is the reason of it ?
>
> Regards
>
>
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: amberquestion_at_yahoo.com; AMBER Mailing List <amber_at_ambermd.org>
> Sent: Monday, February 16, 2009 10:41:54 PM
> Subject: Re: [AMBER] using ptraj
>
> it can be done with ptraj and a bit of extra work, but the important
> thing is that you need to have saved velocities separately in the MD,
> they are none in the coordinate trajectory file. if you set ntwv to
> the same as ntwx, it can be done.
>
>
>
> On Mon, Feb 16, 2009 at 3:31 PM, Molecular Dynamics
> <amberquestion_at_yahoo.com> wrote:
>> Dear All,
>>
>> Is it possible to extract a snapshot ( coordinates, box size and alpha, beta gamma angles information ) with velocity information from any Amber trajectory files with ptraj and saving this like a restart file ?
>>
>> Regards,
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> hasEML = false;
>>
>>
>>
>>
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>>
>
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