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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
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