Hi
Iam a newby with Rosie, I sent a PDB and sdf file with many molecules for Rosie docking, and I got the following input error message:
Job 「№15623」has failed with the message:
molfile_to_params step failed, please double check your input files!
I searched the documentation and for what I know the input PDB and the SDF where in correct format, but of course I maybe wrong...
Could you please explain me what exactly is wrong with the input and how to correct it?
ADDITIONALLY
I think I may have found the problem, the hydrogens where missing in the SDF file, I added them with babel, it will work?
Thanks a lot,
Fabian Glaser PHD
Technion, Haifa
Israel
Category:
Post Situation:
Unfortunately, that particular job has been deleted, so I can't see the details about why things failed. The fact that the molfile_to_params step failed indicates that it's an issue with the ligand input, though.
I'll mention that *by far* the most common error when doing ligand docking is using the wrong format for the ligand input. While the protein should be in PDB format, the ligand needs to be in SDF/molfile format. See http://ligand-expo.rcsb.org/reports/H/HEM/HEM_ideal.sdf for an example of what a valid SDF file looks like. -- Since you're using babel to convert things, I'm guessing that you probably have that down.
You're right that the ligand should have hydrogens added (for the appropriate pH: deprotonate your carboxylates and protonate your amines) - Using OpenBabel with the "-p" option (or Avogadro with the "Protonate for pH" option) is what I normally do, too. I don't think missing hydrogens would result in an error, though. You'd just get suboptimal docking results.
Other possible errors: Your ligand should be completely connected by bonds. If you have something like a chelated metal ion, you'll need to add a dummy bond (or an extra single bond) from the ligand to the metal ion.
You also should have three dimensional coordinates on your ligand. SDF files from molecular drawing programs sometimes have just 2D coordinates. Those won't do very well in docking, and may confuse the molfile_to_params step.
Hi thanks a lot for the detalied answer.
I tried to add the hydrogens with babel but still get an error, see for example run 15649. But I am puzzled since the hdrogens are there see for example this two molecules from the beginning of the file I am using the approved_hyd.sdf from the drugbank. You can see the full file on the run 15649. I guess there is still something wrong... but what?
Alternatively do you have a built in approved relatively small (thousands) of molecules to dock built in in rosie that I could use for docking?
Best regards,
Fabian
Technion
Haifa, Israel
[NO NAME]
OpenBabel07071510262D
Created with ChemWriter - http://chemwriter.com
175180 0 0 1 0 0 0 0 0999 V2000
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M CHG 1 57 1
M END
> <DATABASE_ID>
DB00014
> <DATABASE_NAME>
drugbank
> <SMILES>
CC(C)C[C@H](NC(=O)[C@@H](COC(C)(C)C)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)[C@H](CO)NC(=O)[C@H](CC1=CNC2=CC=CC=C12)NC(=O)[C@H](CC1=CN=CN1)NC(=O)[C@@H]1CCC(=O)N1)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N1CCC[C@H]1C(=O)NNC(N)=O
> <INCHI_IDENTIFIER>
InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
> <INCHI_KEY>
BLCLNMBMMGCOAS-URPVMXJPSA-N
> <JCHEM_ACCEPTOR_COUNT>
18
> <JCHEM_AVERAGE_POLARIZABILITY>
131.22118283534343
> <JCHEM_BIOAVAILABILITY>
0
> <JCHEM_DONOR_COUNT>
17
> <JCHEM_EXACT_MASS>
1268.641439486
> <JCHEM_FORMAL_CHARGE>
0
> <JCHEM_FORMULA>
C59H84N18O14
> <JCHEM_GHOSE_FILTER>
0
> <JCHEM_IUPAC>
(2S)-1-[(2S)-2-[(2S)-2-[(2R)-3-(tert-butoxy)-2-[(2S)-2-[(2S)-3-hydroxy-2-[(2S)-2-[(2S)-3-(1H-imidazol-5-yl)-2-{[(2S)-5-oxopyrrolidin-2-yl]formamido}propanamido]-3-(1H-indol-3-yl)propanamido]propanamido]-3-(4-hydroxyphenyl)propanamido]propanamido]-4-methylpentanamido]-5-[(diaminomethylidene)amino]pentanoyl]-N-(carbamoylamino)pyrrolidine-2-carboxamide
> <ALOGPS_LOGP>
0.30
> <JCHEM_LOGP>
-5.17557331843203
> <ALOGPS_LOGS>
-4.65
> <JCHEM_MASS>
1269.4105
> <JCHEM_MDDR_LIKE_RULE>
1
> <JCHEM_NUMBER_OF_RINGS>
6
> <JCHEM_PHYSIOLOGICAL_CHARGE>
2
> <JCHEM_PKA>
9.818594492171766
> <JCHEM_PKA_STRONGEST_ACIDIC>
9.267832115311407
> <JCHEM_PKA_STRONGEST_BASIC>
10.816089522841512
> <JCHEM_POLAR_SURFACE_AREA>
495.8899999999997
> <JCHEM_REFRACTIVITY>
325.83880000000016
> <JCHEM_ROTATABLE_BOND_COUNT>
One of your issues with job 15649 is that your input SDF file contains more than one molecule. Each ROSIE ligand docking run is expecting to get an SDF file with a single chemical species in it. (The multiple structures in the SDF file should be different conformers of the same chemical compound.) If you want to dock multiple ligands, you need to submit multiple jobs. If you're attempting to do high-throughput screening, you're probably better off trying to use Rosetta locally - Rosie isn't set up for HTS docking.
The more proximal cause of your error is that some of your molecules (Porfimer, Ergoloid mesylate, etc.) have '*' for element types for some of their atoms. Rosetta needs to know what the atom types are for the ligand, so having things like '*' isn't going to work. -- Also, not every element is supported. You should be fine with standard CHNOPS based compounds and things like halogens, but once you get into more esoteric metal complexes you may have issues. (The core problem is that Rosetta doesn't know how to evaluate interactions with these complexes.)
Rosetta has a small number of small molecules it knows about, but those are normally biologically based. If you're looking for drug-like molecules, you'll need to supply your own set.
Also, note that 15649 still has an issues with 2D structures. The input structures for ligand docking should already have 3D coordinates added. (The --gen3D option of OpenBabel should do a passable job of generating them.) In fact, you normally want multiple such 3D conformations, varying based on the internal degrees of freedom.