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RE: HETATM_IO



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: 
> []On">mailto:]On Behalf Of Ralf
> Schmid
> Sent: Tuesday, September 24, 2002 6:29 AM
> To: 
> 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
> -----------------------------------------------------------------
>
>
>
>