AMBER Archive (2009)

Subject: Re: [AMBER] using ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 17 2009 - 07:34:33 CST

it says that the mdvel file only has 20 frames- does that make sense?
compare the sizes of your mdcrd and mdvel files. also check to make
sure that ntwx and ntwv were the same.

On Tue, Feb 17, 2009 at 8:31 AM, Molecular Dynamics
<amberquestion_at_yahoo.com> wrote:
> [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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>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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