Comments (10)
fjclark
commented on June 24, 2024
1
Thanks, tagging @annamherz as she is handling the RBFE tutorial.
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lohedges
commented on June 24, 2024
I can load all three files without issue using Sire from the openbiosim conda channel, so I presume that whatever issue you are encountering has since been fixed. Could you try creating an environment as follows to see if ti works for you. (Replace mamba with conda if you are not using it.)
mamba create -n bss-test -c conda-forge -c openbiosim/label/dev biosimspace ambertools
mamba activate bss-test
Now try to read the file in this environment. (I've only added ambertools in case you don't have an external version.)
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lohedges
commented on June 24, 2024
Perhaps I've misunderstood your issue... While I can read all of the files without issue (which sounded like your problem) I can only successfully parametrise the fixed one. I'll look into this.
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noahharrison64
commented on June 24, 2024
Hi Lester,
You're right - I think the issue was that I cannot read in the file. I'll install the most recent version of BSS via openbiosim, apologies for not checking this initially.
So the fixed one has been energy minimised to remove poor H-C bond distance and then had the extra bond block added, very odd that it parameterises this yet the minimised version without the added bond block fails.
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lohedges
commented on June 24, 2024
Yes, it's strange. I'll try to figure out why that is tomorrow. In both cases it will write an intermediate PDB file to use with antechamber and I can't think why that would be differ between the two input SDF files, since the bond block isn't used. I'll take a look at the intermediate files and the actual antechamber error message to see what's gone wrong.
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lohedges
commented on June 24, 2024
I'll install the most recent version of BSS via openbiosim, apologies for not checking this initially.
No problem. The plan is to copy packages between the openbiosim and michellab channels for some period of time so that users can slowly switch over. I've been doing this manually to date, so am assuming the fix has been implemented since the last copy. I'll try to automate this when I get a chance.
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lohedges
commented on June 24, 2024
Okay, the issue is that the ligand loaded from the unfixed SDF file appears to be missing 9 hydrogen atoms, so antechamber fails:
import BioSimSpace as BSS
lig0 = BSS.IO.readMolecules("intermediate_H_minimised.sdf")[0]
lig1 = BSS.IO.readMolecules("fixed_intermediate_H_minimised.sdf")[0]
print(lig0)
<BioSimSpace.Molecule: number=2, nAtoms=20, nResidues=1>
print(lig1)
<BioSimSpace.Molecule: number=3, nAtoms=29, nResidues=1>Here are the PDB files generated by converting the SDFs:
intermediate_H_minimised.pdb
MODEL 1
ATOM 1 C MOL 1 -6.790 -6.037 -15.479 1.00 0.00 C
ATOM 2 C MOL 1 -7.388 -4.768 -15.575 1.00 0.00 C
ATOM 3 C MOL 1 -6.597 -3.638 -15.824 1.00 0.00 C
ATOM 4 C MOL 1 -8.771 -9.188 -16.053 1.00 0.00 C
ATOM 5 C MOL 1 -7.636 -7.187 -15.142 1.00 0.00 C
ATOM 6 C MOL 1 -9.562 -9.518 -14.966 1.00 0.00 C
ATOM 7 C MOL 1 -10.427 -10.608 -15.086 1.00 0.00 C
ATOM 8 C MOL 1 -5.402 -6.166 -15.694 1.00 0.00 C
ATOM 9 C MOL 1 -5.216 -3.757 -15.998 1.00 0.00 C
ATOM 10 C MOL 1 -4.623 -5.022 -15.938 1.00 0.00 C
ATOM 11 CL MOL 1 -9.122 -4.579 -15.423 1.00 0.00 CL
ATOM 12 O MOL 1 -8.157 -7.242 -14.035 1.00 0.00 O
ATOM 13 N MOL 1 -7.895 -8.120 -16.118 1.00 0.00 N
ATOM 14 N MOL 1 -10.511 -11.368 -16.196 1.00 0.00 N
ATOM 15 C MOL 1 -9.716 -11.051 -17.218 1.00 0.00 C
ATOM 16 C MOL 1 -8.854 -9.968 -17.183 1.00 0.00 C
ATOM 17 N MOL 1 -9.832 -11.849 -18.332 1.00 0.00 N
ATOM 18 C MOL 1 -8.885 -11.947 -19.314 1.00 0.00 C
ATOM 19 O MOL 1 -7.834 -11.329 -19.236 1.00 0.00 O
ATOM 20 CL MOL 1 -4.602 -7.721 -15.660 1.00 0.00 CL
ENDMDL
END
fixed_intermediate_H_minimised.sdf:
MODEL 1
ATOM 1 C MOL 1 -6.790 -6.037 -15.478 1.00 0.00 C
ATOM 2 C MOL 1 -7.388 -4.768 -15.575 1.00 0.00 C
ATOM 3 C MOL 1 -6.597 -3.638 -15.824 1.00 0.00 C
ATOM 4 C MOL 1 -8.771 -9.188 -16.052 1.00 0.00 C
ATOM 5 C MOL 1 -7.636 -7.187 -15.142 1.00 0.00 C
ATOM 6 C MOL 1 -9.562 -9.518 -14.966 1.00 0.00 C
ATOM 7 C MOL 1 -10.427 -10.608 -15.086 1.00 0.00 C
ATOM 8 C MOL 1 -5.402 -6.166 -15.694 1.00 0.00 C
ATOM 9 C MOL 1 -5.215 -3.757 -15.998 1.00 0.00 C
ATOM 10 C MOL 1 -4.623 -5.022 -15.938 1.00 0.00 C
ATOM 11 CL MOL 1 -9.122 -4.579 -15.423 1.00 0.00 CL
ATOM 12 O MOL 1 -8.157 -7.241 -14.035 1.00 0.00 O
ATOM 13 N MOL 1 -7.895 -8.119 -16.118 1.00 0.00 N
ATOM 14 N MOL 1 -10.511 -11.368 -16.196 1.00 0.00 N
ATOM 15 C MOL 1 -9.716 -11.050 -17.218 1.00 0.00 C
ATOM 16 C MOL 1 -8.855 -9.967 -17.183 1.00 0.00 C
ATOM 17 N MOL 1 -9.833 -11.849 -18.331 1.00 0.00 N
ATOM 18 C MOL 1 -8.885 -11.947 -19.314 1.00 0.00 C
ATOM 19 O MOL 1 -7.834 -11.330 -19.237 1.00 0.00 O
ATOM 20 CL MOL 1 -4.602 -7.721 -15.660 1.00 0.00 CL
ATOM 21 H MOL 1 -7.061 -2.655 -15.888 1.00 0.00 H
ATOM 22 H MOL 1 -9.561 -8.965 -14.036 1.00 0.00 H
ATOM 23 H MOL 1 -11.079 -10.895 -14.266 1.00 0.00 H
ATOM 24 H MOL 1 -4.608 -2.875 -16.189 1.00 0.00 H
ATOM 25 H MOL 1 -3.549 -5.116 -16.087 1.00 0.00 H
ATOM 26 H MOL 1 -7.391 -8.001 -16.990 1.00 0.00 H
ATOM 27 H MOL 1 -8.279 -9.669 -18.048 1.00 0.00 H
ATOM 28 H MOL 1 -10.565 -12.542 -18.273 1.00 0.00 H
ATOM 29 H MOL 1 -9.146 -12.659 -20.112 1.00 0.00 H
ENDMDL
END
Looking at the two SDF files, it does seem that atoms are missing from the first:
intermediate_H_minimised.sdf:
RDKit 3D
20 21 0 0 0 0 0 0 0 0999 V2000
-6.7904 -6.0372 -15.4785 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.3876 -4.7677 -15.5749 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.5974 -3.6384 -15.8244 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.7714 -9.1880 -16.0528 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.6358 -7.1873 -15.1417 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.5618 -9.5176 -14.9656 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.4274 -10.6079 -15.0863 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.4016 -6.1663 -15.6941 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.2156 -3.7572 -15.9984 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.6234 -5.0225 -15.9385 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.1221 -4.5790 -15.4228 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-8.1572 -7.2415 -14.0347 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.8953 -8.1196 -16.1184 N 0 0 0 0 0 0 0 0 0 0 0 0
-10.5112 -11.3677 -16.1956 N 0 0 0 0 0 0 0 0 0 0 0 0
-9.7163 -11.0507 -17.2176 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.8544 -9.9677 -17.1831 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.8325 -11.8494 -18.3316 N 0 0 0 0 0 0 0 0 0 0 0 0
-8.8851 -11.9465 -19.3144 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.8337 -11.3295 -19.2360 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.6018 -7.7207 -15.6597 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0
2 1 2 0
2 11 1 0
3 2 1 0
4 6 2 0
5 12 2 0
7 6 1 0
8 20 1 0
8 1 1 0
9 10 1 0
9 3 2 0
10 8 2 0
13 4 1 0
13 5 1 0
14 7 2 0
15 16 2 0
15 14 1 0
16 4 1 0
17 15 1 0
18 19 2 0
18 17 1 0
M END
fixed_intermediate_H_minimised.sdf
RDKit 3D
29 30 0 0 0 0 0 0 0 0999 V2000
-6.7903 -6.0370 -15.4783 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.3877 -4.7678 -15.5749 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.5974 -3.6381 -15.8244 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.7715 -9.1879 -16.0521 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.6360 -7.1872 -15.1416 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.5622 -9.5182 -14.9657 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.4274 -10.6081 -15.0865 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.4016 -6.1663 -15.6940 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.2155 -3.7570 -15.9985 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.6231 -5.0224 -15.9385 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.1222 -4.5791 -15.4227 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-8.1568 -7.2411 -14.0349 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.8949 -8.1192 -16.1183 N 0 0 0 0 0 0 0 0 0 0 0 0
-10.5111 -11.3680 -16.1963 N 0 0 0 0 0 0 0 0 0 0 0 0
-9.7158 -11.0504 -17.2176 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.8549 -9.9672 -17.1827 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.8327 -11.8492 -18.3314 N 0 0 0 0 0 0 0 0 0 0 0 0
-8.8848 -11.9469 -19.3138 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.8341 -11.3302 -19.2371 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.6019 -7.7209 -15.6597 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-7.0614 -2.6555 -15.8883 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.5606 -8.9651 -14.0355 H 0 0 0 0 0 0 0 0 0 0 0 0
-11.0785 -10.8950 -14.2662 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.6083 -2.8750 -16.1887 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.5488 -5.1163 -16.0871 H 0 0 0 0 0 0 0 0 0 0 0 0
-7.3905 -8.0014 -16.9898 H 0 0 0 0 0 0 0 0 0 0 0 0
-8.2788 -9.6693 -18.0477 H 0 0 0 0 0 0 0 0 0 0 0 0
-10.5649 -12.5422 -18.2734 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.1455 -12.6593 -20.1117 H 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
2 1 2 0 0 0 0
2 11 1 0 0 0 0
3 2 1 0 0 0 0
3 21 1 0 0 0 0
4 6 2 0 0 0 0
5 12 2 0 0 0 0
6 22 1 0 0 0 0
7 6 1 0 0 0 0
7 23 1 0 0 0 0
8 20 1 0 0 0 0
8 1 1 0 0 0 0
9 10 1 0 0 0 0
9 3 2 0 0 0 0
9 24 1 0 0 0 0
10 8 2 0 0 0 0
10 25 1 0 0 0 0
13 4 1 0 0 0 0
13 5 1 0 0 0 0
13 26 1 0 0 0 0
14 7 2 0 0 0 0
15 16 2 0 0 0 0
15 14 1 0 0 0 0
16 4 1 0 0 0 0
16 27 1 0 0 0 0
17 15 1 0 0 0 0
17 28 1 0 0 0 0
18 19 2 0 0 0 0
18 17 1 0 0 0 0
18 29 1 0 0 0 0
M END
$$$$%
Looking at the two files, I think the original issue that you were seeing may be related to this, which is now fixed.
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noahharrison64
commented on June 24, 2024
Ahh that will be my fault - I must have forgotten to set removeHs to false when using rdkit SDMolSupplier prior to energy minimising. I then must have fixed this by copying in the hydrogens that were missing. Not sure how I didn't notice that... Maybe worth including the energy minimised version in the BioSimSpaceTutorials RFBE input data repo for anyone uses that tutorial package in the future.
And good to know about the separator line, will keep an eye on OpenBioSim for future releases and the issues section if anything else crops up for me. Thanks for the help!
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lohedges
commented on June 24, 2024
No problem, glad to hear it's working now. I'll tag in @jmichel80 and @fjclark to let them know about the issue with non-minimised structures in the tutorial.
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noahharrison64
commented on June 24, 2024
Also on that note, I noticed ejm49 was malformed showing an erroneous number of hydrogens with incorrect geometries!
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