Closed vas2201 closed 6 months ago
stefdoerr
commented
6 months ago Hi can you show me how you called the amber.build command please? I am a bit concerned about this "nonterminal" line here
Unknown residue: 5MC number: 105 type: NonterminalIf you can please also share your input structure which you passed to amber.build, call mol.write("./test.pdb") right before and send me the file so I can debug the issue
vas2201
commented
6 months ago Hi Stefdoerr,
Thank you for your response. I have prepared a folder that includes a tRNA subfolder containing the force fields for 5MC (5-methyl-cytosine) and a PDB file, as well as a build amber folder and the Jupyter notebook I am using. I am not entirely certain that these tRNA files meet all the requirements specified by HTMD.
Really appreciate your time and help on this.
Here is google drive link to download the folder. https://drive.google.com/file/d/1fe7i3ZjfFEa1Ij0lv81xONmTMKLHir4x/view?usp=sharing
stefdoerr
commented
6 months ago I managed to get a bit further but I hit this ridiculous error:
Could not find angle parameter for atom types: OR - P - O2
for atom O3' at position -5.911000, -5.164340, 6.998260,
atom P at position -5.832000, -3.815340, 7.884260,
and atom O1P at position -4.478000, -3.733340, 8.477260.but there is obviously no angle between O3', P and O1P. There should be one between O5', P and O1P
So I'm sort of out of ideas. I think the topology of the 5MC residue is just wrong or the PDB names are wrong.
stefdoerr
commented
6 months ago This is the code I used. Practically I disabled capping and added the folder with the parameters to the teleapimports.
mol = Molecule("./2LEB.pdb")
mol.remove("element H")
pmol = systemPrepare(mol)
pmol.set("segid", "P", sel="protein")
pmol.set("name", "O1P", sel='resname "5MC" and name OP1')
pmol.set("name", "O2P", sel='resname "5MC" and name OP2')
amber.build(pmol, ff=amber.defaultFf()+["./tRNA/tRNA.leaprc"], param=["./tRNA/tRNA.frcmod"], topo=["./tRNA/tRNA.in"], teleapimports=['/home/sdoerr/miniforge3/envs/htmd/dat/leap/cmd', '/home/sdoerr/miniforge3/envs/htmd/dat/leap/prep', '/home/sdoerr/miniforge3/envs/htmd/dat/leap/parm', '/home/sdoerr/miniforge3/envs/htmd/dat/leap/lib', "/home/sdoerr/Downloads/debug_folder/tRNA/"], caps={"P": ("none", "none")})Ah I also had to modify tRNA.leaprc to remove these two imports because the first one was already loaded and gave an error and the second trna.pcy does not exist
#parm99 = loadamberparams parm99.dat
#parm99 = loadamberparams trna.pcyThanks for your help on this. I encountered similer error from tleap: Attached pdb coordinates (&atoms) for 5MC for reference below. I corrected the PDB atom names best of my knowledge. Lookslike the error is occurring from force field parameters. Leap.log
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OR - P - O2 for atom O3' at position -5.910162, -5.164340, 6.998260, atom P at position -5.831162, -3.815340, 7.884260, and atom O1P at position -4.477162, -3.733340, 8.477260. ~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OR - P - O2 for atom O3' at position -5.910162, -5.164340, 6.998260, atom P at position -5.831162, -3.815340, 7.884260, and atom O2P at position -7.011162, -3.788340, 8.777260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OR - P - OS for atom O3' at position -5.910162, -5.164340, 6.998260, atom P at position -5.831162, -3.815340, 7.884260, and atom O5' at position -5.986162, -2.610340, 6.823260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OS - P - OQ for atom O3' at position -8.268162, 0.708660, 6.406260, atom P at position -9.803162, 0.922660, 5.963260, and atom OP1 at position -10.673162, 0.604660, 7.118260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OS - P - OQ for atom O3' at position -8.268162, 0.708660, 6.406260, atom P at position -9.803162, 0.922660, 5.963260, and atom OP2 at position -9.998162, 0.198660, 4.692260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OS - P - OR for atom O3' at position -8.268162, 0.708660, 6.406260, atom P at position -9.803162, 0.922660, 5.963260, and atom O5' at position -9.943162, 2.491660, 5.630260. Building proper torsion parameters. Building improper torsion parameters. Warning: No sp2 improper torsion term for CM-CA-CM-CT atoms are: C6 C4 C5 CM5 Warning: No sp2 improper torsion term for NR-CE-CE-ND atoms are: N9 C5 C4 N3 Warning: No sp2 improper torsion term for NB-CF-CE-CE atoms are: N7 C6 C5 C4 Warning: No sp2 improper torsion term for NR-CB-CB-NC atoms are: N9 C5 C4 N3 total 385 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments.
Log.txt
~/anaconda3/envs/htmd2/bin/teLeap: Warning! Parameter file was not saved. quit Quit
Exiting LEaP: Errors = 6; Warnings = 2; Notes = 3.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OR - P - O2 for atom O3' at position -5.910162, -5.164340, 6.998260, atom P at position -5.831162, -3.815340, 7.884260, and atom O1P at position -4.477162, -3.733340, 8.477260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OR - P - O2 for atom O3' at position -5.910162, -5.164340, 6.998260, atom P at position -5.831162, -3.815340, 7.884260, and atom O2P at position -7.011162, -3.788340, 8.777260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OR - P - OS for atom O3' at position -5.910162, -5.164340, 6.998260, atom P at position -5.831162, -3.815340, 7.884260, and atom O5' at position -5.986162, -2.610340, 6.823260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OS - P - OQ for atom O3' at position -8.268162, 0.708660, 6.406260, atom P at position -9.803162, 0.922660, 5.963260, and atom OP1 at position -10.673162, 0.604660, 7.118260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OS - P - OQ for atom O3' at position -8.268162, 0.708660, 6.406260, atom P at position -9.803162, 0.922660, 5.963260, and atom OP2 at position -9.998162, 0.198660, 4.692260.
~/anaconda3/envs/htmd2/bin/teLeap: Error! Could not find angle parameter for atom types: OS - P - OR for atom O3' at position -8.268162, 0.708660, 6.406260, atom P at position -9.803162, 0.922660, 5.963260, and atom O5' at position -9.943162, 2.491660, 5.630260. Building proper torsion parameters. Building improper torsion parameters. total 385 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments.
~/anaconda3/envs/htmd2/bin/teLeap: Warning! Parameter file was not saved. Quit
Exiting LEaP: Errors = 6; Warnings = 2; Notes = 3.
PDB coordinates for 5MC
ATOM 1670 P 5MC B 104 -10.323 0.041 11.325 1.00 0.00 P ATOM 1671 O1P 5MC B 104 -8.969 0.123 11.918 1.00 0.00 O ATOM 1672 O2P 5MC B 104 -11.503 0.068 12.218 1.00 0.00 O ATOM 1673 O5' 5MC B 104 -10.478 1.246 10.264 1.00 0.00 O ATOM 1674 C5' 5MC B 104 -10.346 2.577 10.719 1.00 0.00 C ATOM 1675 C4' 5MC B 104 -10.483 3.624 9.608 1.00 0.00 C ATOM 1676 O4' 5MC B 104 -9.620 3.348 8.525 1.00 0.00 O ATOM 1677 C3' 5MC B 104 -11.884 3.801 9.032 1.00 0.00 C ATOM 1678 O3' 5MC B 104 -12.760 4.565 9.847 1.00 0.00 O ATOM 1679 C2' 5MC B 104 -11.573 4.469 7.710 1.00 0.00 C ATOM 1680 O2' 5MC B 104 -11.440 5.868 7.859 1.00 0.00 O ATOM 1681 C1' 5MC B 104 -10.214 3.876 7.351 1.00 0.00 C ATOM 1682 N1 5MC B 104 -10.458 2.793 6.376 1.00 0.00 N ATOM 1683 C2 5MC B 104 -10.191 3.018 5.035 1.00 0.00 C ATOM 1684 O2 5MC B 104 -9.702 4.084 4.661 1.00 0.00 O ATOM 1685 N3 5MC B 104 -10.482 2.035 4.139 1.00 0.00 N ATOM 1686 C4 5MC B 104 -10.986 0.868 4.550 1.00 0.00 C ATOM 1687 N4 5MC B 104 -11.241 -0.072 3.640 1.00 0.00 N ATOM 1688 C5 5MC B 104 -11.246 0.608 5.928 1.00 0.00 C ATOM 1689 C6 5MC B 104 -10.967 1.600 6.801 1.00 0.00 C ATOM 1690 CM5 5MC B 104 -11.815 -0.725 6.448 0.00 0.00 C
stefdoerr
commented
6 months ago Ah no the topology of 5MC is fine. The issue is the bond to the previous 103 residue. It's missing the parameters to bond the 5MC residue to the RNA C3'. Let me take another look
stefdoerr
commented
6 months ago Yeah the only angles defined including O2 which is the atom type of O1P and O2P are
# in the tRNA.frcmod
O2 - P - HO 0.0 0.00
# These from all_modrna08.frcmod
O2-P -O2 45.1 109.01 same as o -p4-o
O2-P -OS 43.1 110.621 same as o -p4-os
OH-P -O2 42.9 107.128 same as o -p4-ohYou will have to start searching for those parameters unfortunately. I cannot help much more with this.
vas2201
commented
6 months ago Amber Users recommended me to use the following parameters files. These files are available in htmd as well.
amber library file: /home/user/amber/dat/leap/lib/all_modrna08.lib amber parameter file: /home/user/amber/dat/leap/parm/all_modrna08.frcmod
Import those paths in the leap file to test your system building.
I gave try , but end up with issues.
Can you provide me code snippet to source these files properly , if possible ?
Thanks for your help on this.
stefdoerr
commented
6 months ago amber.build(mol, ff=amber.defaultFf()+["./tRNA/tRNA.leaprc", "leaprc.modrna08"], param=["./tRNA/tRNA.frcmod"], topo=["./tRNA/tRNA.in"], teleapimports=['/home/sdoerr/miniforge3/envs/htmd/dat/leap/cmd', '/home/sdoerr/miniforge3/envs/htmd/dat/leap/prep', '/home/sdoerr/miniforge3/envs/htmd/dat/leap/parm', '/home/sdoerr/miniforge3/envs/htmd/dat/leap/lib', "/home/sdoerr/Downloads/debug_folder/tRNA/"], ionize=False)
You just add leaprc.modrna08 to the ff argument list Doesn't help though at least in my case
vas2201
commented
6 months ago Can you provide further assistance on how to solvate and ionize the system?.
stefdoerr
commented
6 months ago Congratulations! Now for solving and ionizing, before building just do
smol = solvate(pmol)
bmol = amber.build(smol, ...., ionize=True)Depending on how you want to solvate (cube or cuboid) you can use either the pad argument to solvate which will just add water padding around the solute or use the minmax argument where you specify the minimum and maximum coordinates of the box.
See the building tutorial here for more details: https://software.acellera.com/htmd/tutorials/system-building-protein-ligand.html#solvate
vas2201
commented
6 months ago How can I use magnesium chloride as ions instead of sodium chloride as ions for the system ?. Thank you.
stefdoerr
commented
6 months ago saltcation="Mg2+"
vas2201
commented
6 months ago Thanks for your help ! you can close this ticket.
stefdoerr
commented
6 months ago Great :)
Dear Support Team,
I have successfully located and downloaded the amber force fields for 5-methyl cytosine (5MC) for RNA from the following database: Amber Manchester Nucleic Acids : http://amber.manchester.ac.uk/nuc/
The files I accessed include:
tRNA.leaprc tRNA.lib tRNA.readme tRNA_inf.html tRNA.frcmod
I then proceeded to rename and copy these files into the respective directories within my HTMD2 environment, structured as follows:
leaprc file: ~/anaconda3/envs/htmd2/dat/leap/cmd/leaprc.tRNA lib file: ~/anaconda3/envs/htmd2/dat/leap/lib/tRNA.lib frcmod file: ~/anaconda3/envs/htmd2/dat/leap/parm/tRNA.frcmod After creating the 5-methyl cytosine structure for target RNA using PyMOL, I loaded it into Amber using default force fields, confirmed by the successful execution of amber.listFiles().
However, I am encountering an error as detailed in the log files within the builder-amber .
I would appreciate any guidance on how to resolve this issue.
Thank you for your attention to this matter. I look forward to your prompt response and solution.
Log.txt file from build-amber folder