input file is as follows
*
*
*trajin fimd.mdcrd*
*rms first mass out m22g_calc_backbone.rms .P,O5', C5', C4', C3', O3', time
0.2.*
the input trajectory is in the same folder where i am running the ptraj
command.
---------- Forwarded message ----------
From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
Date: Tue, Dec 27, 2011 at 11:42 AM
Subject: Re: [AMBER] Fwd: WARNING in ptraj(): No input trajectories
specified (trajin), aborting...
To: AMBER Mailing List <amber.ambermd.org>
Can you mention your input. Is the input trajectory in the same folder
where you are running the ptraj command?
Debostuti
On 12/27/11, rosy stone <stonerosy.gmail.com> wrote:
> From: rosy stone <stonerosy.gmail.com>
> To: amber.ambermd.org
> Cc:
> Date: Tue, 27 Dec 2011 11:02:22 +0530
> Subject: WARNING in ptraj(): No input trajectories specified (trajin),
> aborting...
> Hi everybody,
>>
>> Aftr running MD for my tRNA seq in explicit solvent nw m analysing the
> results. when m
>> runing ptraj files m getting follwing warnings for RMSD calculation:
>>
>> \-/
>
> -/- PTRAJ: a utility for processing trajectory files
>
> /-\
>
> \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
>
> -/- Executable is: "ptraj"
>
> /-\
>
> \-/ Residue labels:
>
>
> RG5 RC RG RG RA RU RU RU RA3 RC5
>
> RU RC RA RG3 RG5 RG RG RA RG RA
>
> RG RC3 RC5 RC RA RG RA3 RU3 RA5 RA3
>
> RA3 RU5 RG RG RA RG3 RU5 RC3 RU5 RG
>
> RU RG3 RC5 RG3 RU5 RC RC RA RC RA
>
> RG RA RA RU RU RC RG RC RA RC
>
> RC RA3 Q2M H2U H2U M2G OMC OMG YG PSU
>
> Q5M Q7M Q5M Q5M PSU Q1M Na+ Na+ Na+ Na+
>
> Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+
>
> ...
>
> Na+ Na+ Na+ Na+ WAT WAT WAT WAT WAT WAT
>
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>
> ...
>
> WAT WAT WAT WAT WAT WAT WAT
>
>
>
> PTRAJ: Processing input from "STDIN" ...
>
>
> PTRAJ: trajin fimd.mdcrd
>
> Checking coordinates: fimd.mdcrd
>
> trajin fimd.mdcrd ignored; could not open file (fimd.mdcrd)
>
>
> PTRAJ: rms first mass out m22g_calc_backbone.rms .P,O5', C5', C4', C3',
> O3', time 0.2
>
> Mask [.P,O5',] represents 138 atoms
>
> WARNING in ptraj(): No input trajectories specified (trajin), aborting...
>
>
>> Is dere smthng wrong? m nt able to interpret above
> *> lines. please help in dis.... **
>
> *
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 27 2011 - 02:30:02 PST
