please forget about this mail: i have found my big mistake fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Sun, Feb 20, 2011 at 6:29 PM
Subject: reimaging failure
To: AMBER Mailing List <amber.ambermd.org>
Hello:
i am trying to reimage TIP3PBOX flying away from an octahedral box
(solvateoct) using ptraj file
trajin density1.mdcrd
trajout density1.reimaged.mdcrd
center : 14607-34785
image familiar
go
where the atoms indicated are for protein and lipid around it. Either
indicating the atoms (please see below the terminal output for this
case) or the corresponding residues (center :110-1382) i get a series
of errors that i don't understand, the warning that no atoms were
selected, and finally segmentation fault.
If no atoms are indicated in the ptraj file (simply "center"), all
atoms are read but still segmentation fault.
Clearly i am far away the correct way. Thanks for (even generic) advice.
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles with hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: angles without hydrogen, KT
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/ hydrogen, IP
Error scanning a value: dihedral w/ hydrogen, ICP
Error scanning a value: dihedral w/ hydrogen, LP
Error scanning a value: dihedral w/ hydrogen, KP
Error scanning a value: dihedral w/ hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: dihedral w/out hydrogen, JP
Error scanning a value: dihedral w/out hydrogen, IP
Error scanning a value: dihedral w/out hydrogen, ICP
Error scanning a value: dihedral w/out hydrogen, LP
Error scanning a value: dihedral w/out hydrogen, KP
Error scanning a value: natex
Error scanning a value: natex
Error scanning a value: natex
Error scanning a value: natex
Error scanning a value: natex
Error scanning a value: natex
Error scanning a value: natex
Error scanning a value: join info
Error scanning a value: join info
Error scanning a value: join info
Error scanning a value: join info
Error scanning a value: irotat info
Error scanning a value: irotat info
Error scanning a value: irotat info
Error scanning a value: irotat info
Error scanning a value: box information, nspsol
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Error scanning a value: box information, nsp
Scanning Cap; this has not been debugged!
Scanning Perturbation info...
Bonds...
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, ibper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Error scanning a value: pert, icbper
Angles...
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ktper
Error scanning a value: pert, itper
Error scanning a value: pert, jtper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Error scanning a value: pert, ictper
Dihedrals...
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, kpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Error scanning a value: pert, icpper
Extra perturbation information...
Error scanning a value: pert, iaper
Error scanning a value: pert, iaper
Error scanning a value: pert, iaper
Error scanning a value: pert, iaper
Error scanning a value: pert, iacper
Error scanning a value: pert, iacper
Error scanning a value: pert, iacper
Error scanning a value: pert, iacper
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin density1.mdcrd
Checking coordinates: density1.mdcrd
PTRAJ: trajout density1.reimaged.mdcrd
PTRAJ: center : 14607-34785
Warning: ':' empty token?
Mask [:] represents 0 atoms !!!NO ATOMS DETECTED!!!
PTRAJ: image familiar
Mask [*] represents 16 atoms
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 506470 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (density1.mdcrd) is an AMBER trajectory with 506470 sets
OUTPUT COORDINATE FILE
File (density1.reimaged.mdcrd) is an AMBER trajectory (with box info)
ACTIONS
1> CENTER to box center via center of geometry, atom selection
follows [No atoms are selected]
2> IMAGE familiar by molecule to box center using the first atom,
atom selection * (All atoms are selected)
IMAGE familiar, center is at box center
Processing AMBER trajectory file density1.mdcrd
Set 1 .Segmentation fault
**********************************8
END MESSAGE
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Received on Sun Feb 20 2011 - 14:00:04 PST
