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PostPosted: Tue Jul 21, 2009 11:17 am 
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Joined: Tue Jul 21, 2009 10:05 am
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Hello,

I am facing an error in AUTODOCK4.0 command line running.

===================================Error========================================
[remya@localhost Flex_AllProtein]$ time autodock4 -p ind_hsg1_rigid.dpf -l ind_hsg1_rigid.dlg
autodock4: ERROR: ERROR: 2750 records read in, but only dimensioned for 2048.
Change "MAX_RECORDS" in "constants.h".
autodock4: Aborting...

autodock4: Unsuccessful Completion.

================================End of the Error===================================

More Information:
Receptor File name: hsg1.pdb [it have 2 chains A and B]
Ligand File: ind.pdb

My need -> i want to give flexibility to all the residue in the protein. Here hsg1.pdb[my receptor] have 2 similar chain, so i selected ChainA's all residue for flexibility (i avoided CYS and MET residues to give flexibilty).

For getting .dlg file [mail autodock output], i used following commands:-
Command 1 : pythonsh prepare_ligand4.py -l ind.pdb
Command 2 : pythonsh prepare_receptor4.py -r hsg1.pdb
Command 3 : pythonsh prepare_flexreceptor4.py -r hsg1.pdbqt -s PRO1_GLN2_ILE3_THR4_LEU5_TRP6_GLN7_ARG8_PRO9_LEU10_VAL11_THR12_ILE13_LYS14_ILE15_GLY16_GLY17_GLN18_LEU19_LYS20_GLU21_ALA22_LEU23_LEU24_ASP25_THR26_GLY27_ALA28_ASP29_ASP30_THR31_VAL32_LEU33_GLU34_GLU35_SER37_LEU38_PRO39_GLY40_ARG41_TRP42_LYS43_PRO44_LYS45_ILE47_GLY48_GLY49_ILE50_GLY51_GLY52_PHE53_ILE54_LYS55_VAL56_ARG57_GLN58_TYR59_ASP60_GLN61_ILE62_LEU63_ILE64_GLU65_ILE66_GLY68_HIS69_LYS70_ALA71_ILE72_GLY73_THR74_VAL75_LEU76_VAL77_GLY78_PRO79_T
HR80_PRO81_VAL82_ASN83_ILE84_ILE85_GLY86_ARG87_ASN88_LEU89_LEU90_THR91_GLN92_ILE93_GLY94_THR96_LEU97_ASN98_PHE99

Command 4 : pythonsh prepare_gpf4.py -l ind.pdbqt -r hsg1_rigid.pdbqt [ my grid centers: 1.833, 5.485, -7.076]
Command 5 : pythonsh prepare_dpf4.py -l ind.pdbqt -r hsg1_rigid.pdbqt -p flexres=hsg1_flex.pdbqt
Command 6 : autogrid4 -p hsg1_rigid.gpf -l hsg1_rigid.glg
Command 7 : autodock4 -p ind_hsg1_rigid.dpf -l ind_hsg1_rigid.dlg

Why this type of error coming (highlight in red color)? I got good result when i selected 1 or 2-4 residue(s) for flexibility. But when i tried with whole residue in a chain, error is showing.

Note: Attached ind_hsg1_rigid.dlg file for reference.


Attachments:
File comment: You can see error in the last part of this .dlg file
ind_hsg1_rigid.dlg [35.96 KiB]
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