Hello AMBER community,
I am developing a DNA system and studying its conformational dynamics with the TCO and TC-Nitro FRET probe pair.
While I work with non-standard residues, I need to create custom force field parameters so that I can use them in the simulations with AMBER.
Up to now, I have:
1.Created individual probe parameters in Antechamber.
2.Tried forming a bond between the modified probe and the DNA in tleap.
Now, the issue I have is that I am getting errors with the bond command in tleap and I do not know what steps to take next.
Errors:
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
Could not find bond parameter for atom types: OS - p4
for atom O3' at position 2.776187, -7.549197, -12.489315
and atom P at position 2.771187, -5.455197, -10.979315.
Building angle parameters.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: OS - p4 - o
for atom O3' at position 2.776187, -7.549197, -12.489315,
atom P at position 2.771187, -5.455197, -10.979315,
and atom O1P at position 3.436187, -6.161197, -9.855315.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: OS - p4 - o
for atom O3' at position 2.776187, -7.549197, -12.489315,
atom P at position 2.771187, -5.455197, -10.979315,
and atom O2P at position 2.913187, -5.960197, -12.357315.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: OS - p4 - os
for atom O3' at position 2.776187, -7.549197, -12.489315,
atom P at position 2.771187, -5.455197, -10.979315,
and atom O5* at position 1.224187, -5.245197, -10.650315.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: CE - OS - p4
for atom C3' at position 2.553187, -6.238197, -12.021315,
atom O3' at position 2.776187, -7.549197, -12.489315,
and atom P at position 2.771187, -5.455197, -10.979315.
Building proper torsion parameters.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
** No torsion terms for atom types: CE-OS-p4-o
for atom C3' at position 2.553187, -6.238197, -12.021315,
atom O3' at position 2.776187, -7.549197, -12.489315,
atom P at position 2.771187, -5.455197, -10.979315,
and atom O1P at position 3.436187, -6.161197, -9.855315.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
** No torsion terms for atom types: CE-OS-p4-o
for atom C3' at position 2.553187, -6.238197, -12.021315,
atom O3' at position 2.776187, -7.549197, -12.489315,
atom P at position 2.771187, -5.455197, -10.979315,
and atom O2P at position 2.913187, -5.960197, -12.357315.
/home/aadarsh/.conda/envs/AmberTools23/bin/teLeap: Error!
** No torsion terms for atom types: CE-OS-p4-os
for atom C3' at position 2.553187, -6.238197, -12.021315,
atom O3' at position 2.776187, -7.549197, -12.489315,
atom P at position 2.771187, -5.455197, -10.979315,
and atom O5* at position 1.224187, -5.245197, -10.650315.
Building improper torsion parameters.
total 332 improper torsions applied
I would appreciate any help regarding:
1.The approaches to complete the parameterization and integration of such DNA FRET probes into a DNA system in AMBER.
2.The ion and parameter sets for TCO and TC-Nitro that are used with TLEAP.
3.Inter-residue bond construction in tleap and associated troubleshooting.
Thanks for your assistance in advance!
Sincerely,
Rahul Singal
Undergraduate Student
IIIT Hyderabad
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Received on Wed Mar 26 2025 - 00:00:02 PDT
