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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Received on Mon Dec 26 2011 - 22:00:02 PST
