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 > ----------------------------------------------------------------- > > > >