Great, it works. Many thanks.
in fact my crd file defined as a reference had a bad format as it came
out from VMD. I didn't know that vmd file are not compatible
for calculation with ptraj.
Le 21/03/2011 15:30, Rahul Banerjee a écrit :
> 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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>
>
>
--
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 - 09:00:03 PDT
