Request to Fix Error with 5-Methyl Cytosine amber Force Fields and Suggestion for Improvement about htmd

[stefdoerr]

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: Nonterminal

If 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]

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]

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]

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.pcy

[vas2201]

Thanks 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]

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]

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-oh

You will have to start searching for those parameters unfortunately. I cannot help much more with this.

[vas2201]

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]

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]

I modified the leaprc.modrna08 file by uncommenting the source lines. I am able to build the system without errors.
However, I am encountering issues while solvating and ionizing the system. Can you provide further assistance on how to solvate and ionize the system?.

[stefdoerr]

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]

How can I use magnesium chloride as ions instead of sodium chloride as ions for the system ?. Thank you.

[stefdoerr]

saltcation="Mg2+"

[vas2201]

Thanks for your help ! you can close this ticket.

[stefdoerr]

Great :)