Hello!
One way you can generate the missing parameters is to use the -
parmcal - tool in AMBERTOOLS, for example for the OS - p4 pair, you
first optimize only that particular structure using a high-level QM
method, then measure the bond distance between those two atoms. In a
quick test I made, I obtain the value of 1.592 Ang; with this value
you use parmcal and you obtain a force constant of 352.320 that you
can include in an frcmod file that you can then load in tleap with
loadamberparams:
BOND OS- p4 352.320 1.592
for the angles:
OS - p4 - o 45.731 107.170
OS - p4 - os 43.975 109.690
CE - OS - p4 78.403 119.340
the torsion is a little more tricky and a reasonable approximation is
using GAFF211 values (by analogy), which you can use:
X -OS-p4-X 2 2.100 180.000 2.000
Of course double check your resulting structure to see if everything
looks as expected. Hope that helps!
Rodrigo.
On Wed, Mar 26, 2025 at 12:30 AM Rahul Singal via AMBER
<amber.ambermd.org> wrote:
>
>
> 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 - 08:00:03 PDT
