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Anonymous.
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December 30, 2018 at 11:07 pm #3064
Anonymous
Hello!
I’m not able to generate a score.sc file because something is not allowing me to dock my ligands to my protein. I get the error
Cannot normalize xyzVector of length() zero
Error: [ ERROR ]
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
Here’s an example of my params file. I’ve attached a copy of my ligand/receptor .pdb and my dock.xml as well:
NAME Out
IO_STRING Out Z
TYPE LIGAND
AA UNK
ATOM N1 Nhis X -0.27
ATOM C1 CH1 X 0.12
ATOM C2 aroC X 0.11
ATOM S1 S X -0.03
ATOM S2 S X -0.08
ATOM C3 CH1 X 0.19
ATOM C4 aroC X 0.29
ATOM O1 OOC X -0.27
ATOM N2 Nhis X -0.11
ATOM C5 CH1 X 0.22
ATOM O2 OOC X -0.20
ATOM C6 aroC X 0.02
ATOM C7 aroC X -0.00
ATOM C8 aroC X -0.00
ATOM C9 aroC X -0.00
ATOM C10 aroC X -0.00
ATOM C11 aroC X -0.00
BOND C1 N1
BOND N1 C2
BOND C2 S1
BOND C2 S2
BOND S2 C3
BOND C3 C4
BOND C4 O1
BOND C4 N2
BOND C3 C5
BOND N1 C5
BOND C5 O2
BOND C5 C6
BOND C6 C7
BOND C7 C8
BOND C8 C9
BOND C9 C10
BOND C10 C11
BOND C6 C11
CHI 1 S2 C3 C4 O1
CHI 2 C3 C5 C6 C7
NBR_ATOM N1
NBR_RADIUS 0.000000
ICOOR_INTERNAL N1 0.000000 0.000000 0.000000 N1 C1 C2
ICOOR_INTERNAL C1 0.000000 0.000000 0.000000 N1 C1 C2
ICOOR_INTERNAL C2 0.000000 0.000000 0.000000 N1 C1 C2
ICOOR_INTERNAL S1 0.000000 0.000000 0.000000 C2 N1 C1
ICOOR_INTERNAL S2 0.000000 0.000000 0.000000 C2 N1 S1
ICOOR_INTERNAL C3 0.000000 0.000000 0.000000 S2 C2 N1
ICOOR_INTERNAL C4 0.000000 0.000000 0.000000 C3 S2 C2
ICOOR_INTERNAL O1 0.000000 0.000000 0.000000 C4 C3 S2
ICOOR_INTERNAL N2 0.000000 0.000000 0.000000 C4 C3 O1
ICOOR_INTERNAL C5 0.000000 0.000000 0.000000 C3 S2 C4
ICOOR_INTERNAL O2 0.000000 0.000000 0.000000 C5 C3 S2
ICOOR_INTERNAL C6 0.000000 0.000000 0.000000 C5 C3 O2
ICOOR_INTERNAL C7 0.000000 0.000000 0.000000 C6 C5 C3
ICOOR_INTERNAL C8 0.000000 0.000000 0.000000 C7 C6 C5
ICOOR_INTERNAL C9 0.000000 0.000000 0.000000 C8 C7 C6
ICOOR_INTERNAL C10 0.000000 0.000000 0.000000 C9 C8 C7
ICOOR_INTERNAL C11 0.000000 0.000000 0.000000 C10 C9 C8Thanks,
Patrick
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December 31, 2018 at 1:15 am #14551
I looked back at my .mol2 files for compounds that dock vs those that don’t…. It’s pretty obvious the problem is with the mol files. I used open babel to create the mol files….. Is there some reason why the coordinates read 0 0 0? Here’s an example of the mol file for a compound that does not dock:
@<TRIPOS>MOLECULE
*****
15 16 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 0.0000 0.0000 0.0000 C.3 1 LIG1 0.0398
2 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0282
3 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0694
4 N 0.0000 0.0000 0.0000 N.ar 1 LIG1 -0.2677
5 C 0.0000 0.0000 0.0000 C.2 1 LIG1 0.0835
6 C 0.0000 0.0000 0.0000 C.2 1 LIG1 0.0206
7 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.2958
8 O 0.0000 0.0000 0.0000 O.2 1 LIG1 -0.2591
9 S 0.0000 0.0000 0.0000 S.2 1 LIG1 -0.0300
10 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0164
11 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0015
12 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0000
13 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0000
14 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0000
15 C 0.0000 0.0000 0.0000 C.ar 1 LIG1 0.0015
@<TRIPOS>BOND
1 1 2 1
2 2 3 ar
3 3 4 ar
4 4 5 1
5 5 6 2
6 4 7 ar
7 7 8 2
8 7 9 ar
9 2 9 ar
10 3 10 1
11 10 11 ar
12 11 12 ar
13 12 13 ar
14 13 14 ar
15 14 15 ar
16 10 15 ar
Here’s an example of a compound that successfully docks.
@<TRIPOS>MOLECULE
*****
16 16 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 1.7534 4.2979 0.0000 C.3 1 LIG1 0.0030
2 C 2.4679 3.8854 0.0000 C.3 1 LIG1 0.0348
3 C 2.4679 3.0604 0.0000 C.3 1 LIG1 0.1481
4 O 1.6429 3.0604 0.0000 O.3 1 LIG1 -0.2211
5 C 3.2929 3.0604 0.0000 C.3 1 LIG1 0.0348
6 C 3.7054 2.3459 0.0000 C.3 1 LIG1 0.0030
7 C 2.4679 2.2354 0.0000 C.ar 1 LIG1 0.0392
8 C 3.1823 1.8229 0.0000 C.ar 1 LIG1 0.0042
9 C 3.1823 0.9979 0.0000 C.ar 1 LIG1 0.0369
10 C 2.4679 0.5854 0.0000 C.ar 1 LIG1 0.1417
11 O 2.4679 -0.2396 0.0000 O.3 1 LIG1 -0.4713
12 C 3.1823 -0.6521 0.0000 C.3 1 LIG1 0.2525
13 C 1.7534 0.9979 0.0000 C.ar 1 LIG1 0.0735
14 C 1.7534 1.8229 0.0000 C.ar 1 LIG1 0.1400
15 O 1.0389 2.2354 0.0000 O.3 1 LIG1 -0.4716
16 C 0.3245 1.8229 0.0000 C.3 1 LIG1 0.2525
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 3 5 1
5 3 7 1
6 5 6 1
7 7 8 ar
8 7 14 ar
9 8 9 ar
10 9 10 ar
11 10 11 1
12 10 13 ar
13 11 12 1
14 13 14 ar
15 14 15 1
16 15 16 1
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December 31, 2018 at 6:29 am #14550
I think the error might be related to the coordinates in the paramaters file….. I compared it to compounds I have used before that have successfully docked. These compounds all have coordinates 0 0 0 whereas compounds that have docked successfully actually have non zero values. I’m thinking the problem might be with parameterization….. Here’s the script I use to do the docking.
#!/bin/bash
echo -n “Enter the name of the receptor pdb file:”
read receptor
for files in ligand*.mol2
do
/users/PHS0297/ohu0515/rosetta/main/source/scripts/python/public/molfile_to_params.py -n “Out${files%.mol2}” -p “Out${files%.mol2}” $files
cat $receptor “Out${files%.mol2}_0001.pdb” > “Out${files%.mol2}_wReceptor.pdb”
~/rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease -in:path:database /users/PHS0297/ohu0515/rosetta/main/database/ -in:file:s “Out${files%.mol2}_wReceptor.pdb” -in:file:extra_res_fa “Out${files%.mol2}.params” -out:nstruct 3 -parser:protocol /users/PHS0297/ohu0515/dock.xml
mv “Out${files%.mol2}_wReceptor_0001.pdb” “${files%.mol2}_docked_0001.pdb”
mv “Out${files%.mol2}_wReceptor_0002.pdb” “${files%.mol2}_docked_0002.pdb”
mv “Out${files%.mol2}_wReceptor_0003.pdb” “${files%.mol2}_docked_0003.pdb”
sort -n -k50 score.sc | head -n 100000 | awk ‘{print $2 “t” $50 “t” $NF}’ > reportcardirf3.dat
done
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December 31, 2018 at 6:33 am #14552
I think I resolved my own problem here but wanted to post the solution in case anyone is having a similar problem. The ligands I created using Data Warrior were smiles. When I converted these smiles to .mol2 files using open babel I did not use the –gen3d option. This is essential because rosetta needs the 3d coordinates. Here’s why. http://hjkgrp.mit.edu/content/geometries-strings-smiles-and-openbabel
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December 31, 2018 at 4:58 pm #14553
Your journey of self-discovered-solutions has led you to the correct place. Rosetta is angry that the coordinates are garbage – specifically that the torsion angle between 4 atoms that are all at the origin is undefined. I think your tracing the problem upstream to a bad SMILES->conformation conversion is correct.
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