Topic Options
#499 - 11/13/03 01:14 AM Error message
tjaart Offline
Forum Member

Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa
Hi there

When I try to run I script I get this error and then MPI just terminates.

CHARMM> OPEN UNIT 1 CARD READ NAME LIG.pdb
VOPEN> Attempting to open::LIG.PDB::
OPNLGU> Unit 1 opened for READONLY access to LIG.PDB

CHARMM> READ sequ pdb unit 1
MAINIO> Sequence information being read from unit 1.
TITLE> *
** ERROR IN SEQRDR ** REPEATED RESID FOR 7 9 4.
*** LEVEL 0 WARNING *** BOMLEV IS -1
** ERROR IN SEQRDR ** REPEATED RESID FOR 4 12 -1.
*** LEVEL 0 WARNING *** BOMLEV IS -1
** ERROR IN SEQRDR ** REPEATED RESID FOR 10 13 0.
*** LEVEL 0 WARNING *** BOMLEV IS -1
** ERROR IN SEQRDR ** REPEATED RESID FOR 6 16 3.
*** LEVEL 0 WARNING *** BOMLEV IS -1
** ERROR IN SEQRDR ** REPEATED RESID FOR 15 17 2.
*** LEVEL 0 WARNING *** BOMLEV IS -1

Any ideas on how to fix this?

Thanks!!!!!!
_________________________
Tjaart de Beer

Top
#500 - 11/14/03 11:49 PM Re: Error message [Re: tjaart]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
It's difficult to tell out of context, but it suggests a problem with the PDB format file. From io.doc :

--------------------------
The PDB option works very much like the CARD option, but expects the actual file format to be according to Protein Data Bank standards:

text IATOM TYPE RES IRES X Y Z W
A6 I5 2X A4 A4 I5 4X 3F8.3 6X F6.2
--------------------------

The residue numbers (from IRES field) must be unique, and should be sequential or you may have problems within CHARMM. Make sure the data is in the correct columns, and that the file can be read by other programs such as Rasmol or babel.
_________________________
Rick Venable
computational chemist


Top

Moderator:  John Legato, lennart