Dear All,
For a few days I have been trying to parameterise the following Pt(II) complex (derivative of cisplatin, but in trans and different ligands):
I am trying to base on the tutorials presented on the website (
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php <
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.php>), in the original paper by Prof. Li and Prof. Merz Jr (
https://pubs.acs.org/doi/10.1021/acs.jcim.5b00674 <
https://pubs.acs.org/doi/10.1021/acs.jcim.5b00674>) and the version in the book (
https://link.springer.com/protocol/10.1007/978-1-0716-0892-0_15 <
https://link.springer.com/protocol/10.1007/978-1-0716-0892-0_15>) but I keep running into problems and new questions arise.
First of all, this is what the initial .pdb file looks like (created from the optimised Gauss structure). I believe I followed all the instructions:
HETATM 1 C1 ISO 1 3.004 -0.768 0.006 1.00 0.00 C
HETATM 2 C2 ISO 1 4.225 -0.038 -0.037 1.00 0.00 C
HETATM 3 C3 ISO 1 3.904 1.293 -0.177 1.00 0.00 C
HETATM 4 O1 ISO 1 2.571 1.389 -0.216 1.00 0.00 O
HETATM 5 N1 ISO 1 2.022 0.104 -0.104 1.00 0.00 N
HETATM 6 PT PT 2 0.001 0.009 -0.100 1.00 0.00 Pt
HETATM 7 C4 ISO 1 2.772 -2.231 0.137 1.00 0.00 C
HETATM 8 H1 ISO 1 3.176 -2.577 1.092 1.00 0.00 H
HETATM 9 H2 ISO 1 1.709 -2.463 0.080 1.00 0.00 H
HETATM 10 H3 ISO 1 3.315 -2.755 -0.653 1.00 0.00 H
HETATM 11 C5 ISO 1 4.690 2.540 -0.283 1.00 0.00 C
HETATM 12 H4 ISO 1 5.345 2.487 -1.157 1.00 0.00 H
HETATM 13 H5 ISO 1 4.023 3.399 -0.367 1.00 0.00 H
HETATM 14 H6 ISO 1 5.330 2.645 0.596 1.00 0.00 H
HETATM 15 N2 ISO 1 5.548 -0.571 0.047 1.00 0.00 N
HETATM 16 O2 ISO 1 6.486 0.227 -0.026 1.00 0.00 O
HETATM 17 O3 ISO 1 5.666 -1.790 0.188 1.00 0.00 O
HETATM 18 CL CL 3 0.006 -0.655 2.128 1.00 0.00 Cl
HETATM 19 N1 ISO 4 -2.022 -0.066 -0.128 1.00 0.00 N
HETATM 20 C1 ISO 4 -2.990 0.765 0.202 1.00 0.00 C
HETATM 21 O1 ISO 4 -2.593 -1.276 -0.554 1.00 0.00 O
HETATM 22 C2 ISO 4 -4.223 0.089 -0.017 1.00 0.00 C
HETATM 23 C4 ISO 4 -2.730 2.141 0.702 1.00 0.00 C
HETATM 24 C3 ISO 4 -3.924 -1.170 -0.486 1.00 0.00 C
HETATM 25 N2 ISO 4 -5.536 0.606 0.205 1.00 0.00 N
HETATM 26 H1 ISO 4 -1.660 2.344 0.737 1.00 0.00 H
HETATM 27 H2 ISO 4 -3.228 2.863 0.051 1.00 0.00 H
HETATM 28 H3 ISO 4 -3.163 2.251 1.699 1.00 0.00 H
HETATM 29 C5 ISO 4 -4.731 -2.338 -0.899 1.00 0.00 C
HETATM 30 O2 ISO 4 -6.488 -0.134 -0.054 1.00 0.00 O
HETATM 31 O3 ISO 4 -5.632 1.755 0.641 1.00 0.00 O
HETATM 32 H4 ISO 4 -5.383 -2.055 -1.730 1.00 0.00 H
HETATM 33 H5 ISO 4 -4.080 -3.160 -1.195 1.00 0.00 H
HETATM 34 H6 ISO 4 -5.376 -2.647 -0.072 1.00 0.00 H
HETATM 35 O1 WAT 5 0.052 0.645 -2.153 1.00 0.00 O
HETATM 36 H1 WAT 5 -0.292 -0.035 -2.755 1.00 0.00 H
HETATM 37 H2 WAT 5 -0.485 1.442 -2.298 1.00 0.00 H
(the mailing cause spaces, but the file is fine here)
At this stage I have the following questions:
1) Can I parameterise the "ligands" on the basis of one molecule, if they are the same? Only the residue identifier needs to be changed in the final pdb as I have done, right?
2) I understand that the platinum should be moved to an external .pdb, dedicated to the metal ion itself. Should I do the same with Cl? The charge of the whole system is +1.
...In general, I should have ISO.mol2, PT.mol2, WAT.mol2 and CL.mol2, right?
Presuming I was right so far, the following input is used for parameters generation:
original_pdb PTT.pdb
group_name PTT
cut_off 2.8
ion_ids 6 18
ion_mol2files PT.mol2 CL.mol2
naa_mol2files ISO.mol2
frcmod_files ISO.frcmod
I get the input files for Gaussian. I upload them in Gaussian16 changing only to GENECP and SDD for Pt. However, when I go to step -s 2 I get a strange error about dividing by zero. And I cannot get around it in any way. Here I would already ask for a hint on what I did wrong? The Gaussian output files .log and .fchk are fine!
Thank you in advance
Sincerely
--
Maciej Spiegel, MPharm
Department of Pharmacognosy and Herbal Medicines
Wroclaw Medical University
https://farmaceut.github.io <https://farmaceut.github.io/>
.ORCiD <https://orcid.org/0000-0002-8012-1026> .Publons <https://publons.com/researcher/4419515/maciej-spiegel/>
Reviewer at:
Phytochemistry | Free Radical Research | Theoretical Chemistry Accounts
Journal of Molecular Modeling | Frontiers in Bioscience-Landmark | Symmetry
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Received on Wed May 31 2023 - 09:00:03 PDT
