Dear Muriel,
You can try to define a PDB file as reference. In that case generate the reference file using ambpdb if necessary.
Best,
Rahul
________________________________________
From: Muriel Jourdan [Muriel.Jourdan.ujf-grenoble.fr]
Sent: Monday, March 21, 2011 10:28 AM
To: amber.ambermd.org
Subject: [AMBER] probleme with "reference" using ptraj
Hi everybody
I would like to calculate a rmsd using a molecule
as a reference but I do have problems as the molecule
defined as a reference is not read and it does not produce output
files. It seems that colleagues have already encoutered this problems
but in my case I do not manage to fixe it.
Thanks for your help
here is the script I've used and the errors
messages:
script:
trajin mTTdyn1.mdcrd
reference mTTdyn-249.crd
rms reference out tutu.rmsfit .P,O3',O5',C3',C4',C5'
issue:
PTRAJ: trajin mTTdyn1.mdcrd
Checking coordinates: mTTdyn1.mdcrd
PTRAJ: reference mTTdyn-249.crd
Processing AMBER trajectory file mTTdyn-249.crd
PTRAJ: rms reference out tutu.rmsfit .P,O3',O5',C3',C4',C5'
WARNING in ptraj(), rms to reference: missing reference structure.
Set this prior to this rms with the command "reference"
Ignoring command...
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 250 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (mTTdyn1.mdcrd) is an AMBER trajectory with 250 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
--
Muriel JOURDAN
Département de Chimie Moléculaire
Batiment Nanobio
570 rue de la Chimie
BP 53 38041 GRENOBLE Cedex 9
Tel : (+00 33) (0)4 56 52 08 39
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Received on Mon Mar 21 2011 - 08:00:03 PDT
