[AMBER] probleme with "reference" using ptraj

From: Muriel Jourdan <Muriel.Jourdan.ujf-grenoble.fr>
Date: Mon, 21 Mar 2011 15:28:09 +0100

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
D├ępartement de Chimie Mol├ęculaire
Batiment Nanobio
570 rue de la Chimie
BP 53 38041 GRENOBLE Cedex 9
Tel : (+00 33) (0)4 56 52 08 39
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 21 2011 - 07:30:04 PDT
Custom Search