That must be the problem. Take note that in the pdb file, the a.a. residues have a chain identifier as well while the cofactor has none.
kind regards, jonathan
--- Roberto Sanchez roberto.sanchez@mssm.edu skrev: > Hi, > > Try explicit naming of the residue numbers in the > structureX line of the > .ali file (including the FAD residue). > > Best, > > Roberto > > -- > Roberto Sanchez, Assistant Professor > Structural Biology Program, Department of Physiology > & Biophysics and > Institute for Computational Biomedicine, Mount Sinai > School of Medicine > Box 1677, 1425 Madison Avenue, New York, NY 10029 > phone +1 (212) 659 8648, fax +1 (212) 849 2456 > http://physbio.mssm.edu/~sanchez/ > > > -----Original Message----- > > From: owner-modeller_usage@salilab.org > > > [mailto:owner-modeller_usage@salilab.org]On > Behalf Of Ralf > > Schmid > > Sent: Tuesday, September 24, 2002 6:29 AM > > To: modeller_usage@salilab.org > > Subject: HETATM_IO > > > > > > > > Dear all, > > > > > > I'm trying to model a protein including a > cofactor, but get an error > > message pointing towards problems in the alignment > and/or pdb file. > > Modelling without cofactor (i.e. removing "/." > from the alignment file) > > works fine. I can't figure out what causes the > problem. > > > > Any help will be appreciated, please see the files > below. > > > > Thanks in advance, > > > > ralf > > > > > > xxx.log: > > <snip> > > TOP_________> 120 106 READ_ALIGNMENT FILE = > ALNFILE, ALIGN_CODES = KNOWNS > > SEQUE; > > NCE > > Dynamically allocated memory at amaxseq > [B,kB,MB]: > > 2205269 2153.583 2.103 > > openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali > > openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb > > Dynamically allocated memory at amaxbnd > [B,kB,MB]: > > 9440821 9219.552 9.003 > > openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali > > openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb > > rdpir___648E> Alignment sequence not found in PDB > file: 1 ./yyy.pdb > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > > > xxx.top: > > INCLUDE > > SET OUTPUT_CONTROL= 1 1 1 1 1 > > SET ALNFILE = 'xxx.ali' > > SET KNOWNS = 'yyy' > > SET SEQUENCE = 'xxx' > > SET STARTING_MODEL = 20 > > SET ENDING_MODEL = 20 > > SET HETATM_IO = on > > CALL ROUTINE = 'model' > > > > > > xxx.ali: > > >P1;xxx > > sequence:xxx:.:.:.:.:.:.:.:. > > VKNER/.* > > >P1;yyy > > structureX:yyy:.:.:.:.:.:.:.:. > > VKQER/.* > > > > > > yyy.pdb: > > <snip> > > ATOM 3488 OXT ARG A 447 31.403 66.404 > 103.394 1.00 65.84 O > > TER 3489 ARG A 447 > > HETATM 3490 AP FAD 448 60.780 56.948 > 67.003 1.00 33.65 P > > <snip> > > > > > > > > > ----------------------------------------------------------------- > > Dr. Ralf Schmid > > ICMB > > The University of Edinburgh > > Michael Swann Building 3.14 > > > ----------------------------------------------------------------- > > > > > > > > > >
===== Jonathan LS Esguerra Structural Chemistry Department of Medical Biochemistry Gothenburg University, Sweden
_____________________________________________________ Gratis e-mail resten av livet på www.yahoo.se/mail Busenkelt!