Hi,
Have you checked if these are the parameters that you want to have for 5MC.
If you look at the prepin file, the atoms are not exactly matching with the
atoms of 5MC. I told you earlier they have written that these are
for deoxy-5-methylcytosine.
*Best,*
*Satyajit Khatua*
On Wed, May 8, 2024 at 11:52 PM Penumutchu, Srinivasa <
Srinivasa.Penumutchu.pennmedicine.upenn.edu> wrote:
> Thank you for your reply.
>
>
>
> I'm currently using HTMD and have sourced all the tRNA files for
> 5-Methylcytosine parameters (http://amber.manchester.ac.uk/). However,
> I'm encountering an error from tleap:
>
> Attached pdb coordinates (&atoms) for 5MC for reference below.
>
> 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
>
>
>
> *From:* SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
> *Sent:* Tuesday, May 7, 2024 10:38 AM
> *To:* Penumutchu, Srinivasa <Srinivasa.Penumutchu.Pennmedicine.upenn.edu>;
> AMBER Mailing List <amber.ambermd.org>
> *Subject:* [External] Re: Amber force fields for 5-Methylcytosine
> Nucleotide RNA
>
>
>
> Hi,
>
>
>
> Look into the nucleic acid section of http://amber.manchester.ac.uk/ if
> you find anything. There is one deoxy 5-Methylcytosine parameters. But I
> don't know if that is what you enquired about.
>
>
>
> Best,
>
> Satyajit
> ------------------------------
>
> *From:* Penumutchu, Srinivasa via AMBER <amber.ambermd.org>
> *Sent:* Tuesday, May 7, 2024 10:26:28 AM
> *To:* amber.ambermd.org <amber.ambermd.org>
> *Subject:* [AMBER] Amber force fields for 5-Methylcytosine Nucleotide RNA
>
>
>
> Dear all,
>
> I'm reaching out to request force field parameters for Naturally
> Occurring Modified Nucleosides in RNA. More specifically, looking for
> 5-Methylcytosine Nucleotide for RNA.
>
> Could you kindly share a valid link or resource from which I can download
> these parameters?.
>
> Regards,
>
> Vas
>
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>
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Received on Thu May 09 2024 - 09:30:02 PDT
