Open kunal19977835 opened 1 month ago
can you post the files?
and list the missing atoms and incorrect bonds
test.zip i've uploaded the dlg file, along with original protein structure (SOD) and the rigid protein and flex protein files. not able to combine as there are some atoms missing in the rigid protein file and when I combine using original protein file (SOD) in pdb format, it shows multiple bonds in chimera
In a docking with flexible sidechains, the protein is split into two PDBQT files, one for the static atoms (suffixed with _rigid) and another for the movable sidechain atoms (suffixed with _flex). Unfortunately, we don't have a script to rebuild an entire protein updated with the docked positions of the sidechain, but that will be implemented soon and released in v0.6. Meanwhile, if you load the rigid part and the docked SDFs into a viewer, it's likely that the bonds between the flexible sidechain and the rest of the protein are missing because they are in different objects.
Is there any other way to work around this problem?
Two laborious ways come to mind:
test1.zip I already tried that, but when i uploaded this file in schrodinger maestro, I could see multiple bonds which showed errors. Can you please look at it?
Hi @kunal19977835 The hydrogen named 1HC is too close to the carbonyl oxygen of Val146. This is because the hydrogen is nonpolar (therefore treated implicitly) in AutoDock. When you import this PDB file, schrodinger maestro attempts to guess bonds based on proximity. To resolve the conflicts, you could edit the bond manually, then run a minimization in maestro
![Uploading IMG_4608.jpeg…] ![Uploading IMG_4609.jpeg…] I adjusted bond length as you asked, but still got these errors
Looks like Maestro is creating non existing bonds based on atom names. For example, the bond between backbone N and the H on the carboxylic acid is probably being hallucinated because both of these hydrogens are named "H".
Hi @kunal19977835
Could you tell us a little bit more about how you generated cys.pdb
?
When you import this structure in maestro, you will see the following problems with atom names:
WARNING mmpdb_build_altloc_db_for_atom: Atom records 78 and 79 in residue 6 (CYS ), chain 'A' have same name ' C '
WARNING mmpdb_build_altloc_db_for_atom: Atom records 78 and 80 in residue 6 (CYS ), chain 'A' have same name ' C '
WARNING mmpdb_build_altloc_db_for_atom: Atom records 78 and 81 in residue 6 (CYS ), chain 'A' have same name ' C '
WARNING mmpdb_build_altloc_db_for_atom: Atom records 82 and 83 in residue 6 (CYS ), chain 'A' have same name ' O '
WARNING mmpdb_build_altloc_db_for_atom: Atom records 82 and 84 in residue 6 (CYS ), chain 'A' have same name ' O '
WARNING mmpdb_build_altloc_db_for_atom: Atom records 86 and 87 in residue 6 (CYS ), chain 'A' have same name ' S '
WARNING mmpdb_build_altloc_db_for_atom: Atom records 88 and 89 in residue 6 (CYS ), chain 'A' have same name ' H '
Imported 1 structure
You can also use Protein Preparation > View Problems to view these problems. The unexpected names are causing atom typing issue for maestro, because CYS is a standard residue and has a certain template in maestro. The quick way to fix it is to rename the atoms (maybe using other CYS in your system as a template, and definitely isolate the covalent conjugate as a new residue).
How do I do that?
I used meeko to align homocysteine as a ligand and bound it with 6th cysteine residue, then used covalent docking scripts from autodock. Rest the problem I’m facing I’ve reported earlier in this tread
@kunal19977835 since this is an issue with Maestro, you could contact their support team.
@kunal19977835 Do you think (in any import/export steps) meeko might have dropped the atom names?
I don’t know, could be covalent bond scripts from autodock. Can you suggest me some work around to fix these? Like which software to use and how
Hi @kunal19977835 It's easy to manually fix the atom names, if you don't have too many atom names missing. This requires some basic knowledge on the standard atom names and the PDB format. To do this, just open the file in a text editor, then change the atom names. From this:
ATOM 77 N CYS A 6 20.631 75.490 11.558 1.00 0.00 N
ATOM 78 C CYS A 6 18.860 75.944 9.976 1.00 0.00 C
ATOM 79 C CYS A 6 17.860 73.952 11.545 1.00 0.00 C
ATOM 80 C CYS A 6 17.722 72.545 10.980 1.00 0.00 C
ATOM 81 C CYS A 6 19.032 71.814 11.122 1.00 0.00 C
ATOM 82 O CYS A 6 19.320 76.992 9.526 1.00 0.00 O
ATOM 83 O CYS A 6 20.048 72.277 11.611 1.00 0.00 O
ATOM 84 O CYS A 6 18.978 70.557 10.627 1.00 0.00 O
ATOM 85 CB CYS A 6 18.589 76.525 12.438 1.00 0.00 C
ATOM 86 S CYS A 6 16.793 76.684 12.191 1.00 0.00 S
ATOM 87 S CYS A 6 16.345 74.915 11.236 1.00 0.00 S
ATOM 88 H CYS A 6 21.145 76.215 11.072 1.00 0.00 H
ATOM 89 H CYS A 6 18.108 70.311 10.260 1.00 0.00 H
ATOM 90 1HC CYS A 6 18.034 73.892 12.619 1.00 0.00 H
ATOM 91 2HC CYS A 6 18.706 74.449 11.071 1.00 0.00 H
ATOM 92 3HC CYS A 6 16.946 72.009 11.527 1.00 0.00 H
ATOM 93 4HC CYS A 6 17.450 72.602 9.926 1.00 0.00 H
To this:
ATOM 77 N CYS A 6 20.631 75.490 11.558 1.00 0.00 N
ATOM 78 C CYS A 6 18.860 75.944 9.976 1.00 0.00 C
ATOM 79 C1 LIG A 152 17.860 73.952 11.545 1.00 0.00 C
ATOM 80 C2 LIG A 152 17.722 72.545 10.980 1.00 0.00 C
ATOM 81 C3 LIG A 152 19.032 71.814 11.122 1.00 0.00 C
ATOM 82 O LIG A 152 19.320 76.992 9.526 1.00 0.00 O
ATOM 83 O1 LIG A 152 20.048 72.277 11.611 1.00 0.00 O
ATOM 84 O2 LIG A 152 18.978 70.557 10.627 1.00 0.00 O
ATOM 85 CB CYS A 6 18.589 76.525 12.438 1.00 0.00 C
ATOM 86 SG CYS A 6 16.793 76.684 12.191 1.00 0.00 S
ATOM 87 S1 LIG A 152 16.345 74.915 11.236 1.00 0.00 S
ATOM 88 H CYS A 6 21.145 76.215 11.072 1.00 0.00 H
ATOM 89 1HO2 LIG A 152 18.108 70.311 10.260 1.00 0.00 H
ATOM 90 1HC1 LIG A 152 18.034 73.892 12.619 1.00 0.00 H
ATOM 91 2HC1 LIG A 152 18.706 74.449 11.071 1.00 0.00 H
ATOM 92 1HC2 LIG A 152 16.946 72.009 11.527 1.00 0.00 H
ATOM 93 2HC2 LIG A 152 17.450 72.602 9.926 1.00 0.00 H
cys_mod.pdb.txt
You can change ATOM
to HETATM
for LIG atoms if you want, but it doesn't matter to maestro. Now, if you load this structure in maestro, you will not get the same errors. However, there are still bonds to correct, hydrogens to add (for CA and CB), and you may do it in maestro (you can look it up from the maestro manual or a basic tutorial). Follow the basic procedure of "Protein Preparation Wizard" in maestro would be a good start.
Many software (Schrodinger, Amber) still use atom names for parameterization. It's important to have the correct atom names and residue names as required by the software. If your docking input were generated from Meeko and no further changes were done, I do think it's some part of Meeko that unintentionally dropped the atom names. Based on the DLG you posted, the only sidechain atom name kept for CYS 6 is CB and that's indeed very confusing the reactive atom's original name (SG) is overridden and the covalent ligand may have redundant atom names. Redundant atom names might cause issues when they're in the same residue. We will look into that in the near future. Thanks for the reporting
Thank you so much, I’ll try and get back to you if this works
The structure is fixed thank you, can you guide me through steps to perform md simulation of this covalently docked ligand using gromacs. i am facing certain errors
That's an excellent question, we have been working on that and will publish tutorials in the near future, but they are not ready yet. For sure we will cover openmm, and I think it should be possible to convert the input to gromacs.
Is there a work around meanwhile I can work on, I have read that certain people are suggesting adding modified residues in the force fields along with defining sulphide bonds.But since I am. Novice i’m facing issues writing.rtp files and making necessary changes
Hello @kunal19977835
Just a quick note: You don't have to use this docked conformation for parameter generation, or you must do some level of optimization before using it for simulation. The docked conformation appears to be very strained, and this could cause problems if your parameter derivation protocol uses the input geometry for atom typing or parameter verification. There are different ways to set up system with covalent ligands depending on what force field you want. If you want to use the CHARMM36 force field for your system, consider running a CGenFF (https://cgenff.silcsbio.com/) job for the cys-ligand conjugate (or Desaminozystin). Then compare the stream file with the expected .rpt format GROMACS needs. It's best to ask and discuss on the GROMACS forum for technical details: https://gromacs.bioexcel.eu/
Another thing I noticed in the dlg file (which might partly explain the strained conformation..) is:
INPUT FLEXIBLE RESIDUES PDBQT FILE:
___________________________________
INPUT-FLEXRES-PDBQT: BEGIN_RES CYS A 6
INPUT-FLEXRES-PDBQT: REMARK 2 active torsions:
INPUT-FLEXRES-PDBQT: REMARK status: ('A' for Active; 'I' for Inactive)
INPUT-FLEXRES-PDBQT: REMARK 1 A between atoms: CB and S
INPUT-FLEXRES-PDBQT: REMARK 2 A between atoms: S and S
INPUT-FLEXRES-PDBQT: ROOT
INPUT-FLEXRES-PDBQT: ATOM 1 CB CYS A 6 18.589 76.525 12.438 1.00 0.00 0.069 C
INPUT-FLEXRES-PDBQT: ENDROOT
INPUT-FLEXRES-PDBQT: BRANCH 1 2
INPUT-FLEXRES-PDBQT: ATOM 2 S CYS A 6 16.793 76.684 12.191 1.00 0.00 -0.082 SA
INPUT-FLEXRES-PDBQT: BRANCH 2 3
INPUT-FLEXRES-PDBQT: ATOM 3 S CYS A 6 16.275 77.972 13.713 1.00 0.00 -0.082 SA
INPUT-FLEXRES-PDBQT: ATOM 4 C CYS A 6 16.980 79.538 13.107 1.00 0.00 0.080 C
INPUT-FLEXRES-PDBQT: ATOM 5 C CYS A 6 16.646 80.677 14.060 1.00 0.00 0.107 C
INPUT-FLEXRES-PDBQT: ATOM 6 C CYS A 6 17.354 81.931 13.615 1.00 0.00 0.153 C
INPUT-FLEXRES-PDBQT: ATOM 7 O CYS A 6 18.085 82.021 12.644 1.00 0.00 -0.649 OA
INPUT-FLEXRES-PDBQT: ATOM 8 O CYS A 6 17.105 82.981 14.430 1.00 0.00 -0.776 OA
INPUT-FLEXRES-PDBQT: ATOM 9 H CYS A 6 16.508 82.775 15.173 1.00 0.00 0.167 HD
INPUT-FLEXRES-PDBQT: ENDBRANCH 2 3
INPUT-FLEXRES-PDBQT: ENDBRANCH 1 2
INPUT-FLEXRES-PDBQT: END_RES CYS A 6
The 3-Mercaptopropionic acid part is completely flat in 3D and does not have flexible torsions. This may or may not be something you want, and might cause subsequent problems in parameter derivation
I performed covalent docking using meeko and autodock, When I received the results the dlg file seems to be missing some atoms. I’m not able to create a file for md simulation because it shows incorrect bonds and atoms