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