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
Received on Mon Nov 18 2002 - 07:29:21 PST
