AMBER Archive (2002)

Subject: creating a pdb trajectory with carnal

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Nov 18 2002 - 09:29:21 CST

dear Amber users,
   I am trying to create a trajectory with pdbs using carnal.
I have the following input file:

FILES_IN
   PARM p1 ../../rna_ion_wat.top;
   STREAM s1 ../../rna_ion_wat_mdeq_final.mdcrd.gz
             ../../rna_ion_wat_mdprd00.mdcrd.gz
         ../../rna_ion_wat_mdprd01.mdcrd.gz
         ../../rna_ion_wat_mdprd02.mdcrd.gz
         ../../rna_ion_wat_mdprd03.mdcrd.gz
         ../../rna_ion_wat_mdprd04.mdcrd.gz
         ../../rna_ion_wat_mdprd05.mdcrd.gz
         ../../rna_ion_wat_mdprd06.mdcrd.gz;
FILES_OUT
   COORD crd trajectory.pdb PDB;
   COORD crd1 trajectory.pdb APPEND PDB;
DECLARE
   GROUP g1 (RES 1-17);
   IMAGE img g1%cmass;
   RMS fit2 FIT g1 s1 ref;
OUTPUT
   COORD crd fit2 SELECT (1) GROUP g1;
   COORD crd1 fit2 SELECT (2-) GROUP g1;
END

I receive an error message that says that the APPEND or BLANK options
are available only for CRD file format.

Error in PDB_TRAJ.IN line 13: COORD: BLANK or APPEND given w/ non-CRD
format
    Last token was ;

Is that the case? And if yes does anyone know a trick that can do that
directly with carnal. Or should I use a perl script to concatenate the
output pdbs from carnal?
Thanks a lot for replies
Vlad 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204