Hi, I'm working on an inorganic metal-ligand (Cisplatin) and want to perform Molecular dynamics of my ligand with some proteins. The problem is cant parametrize cisplatin, I used swissparam but throw me errors, try with the charmm topology files ( top_all22_prot_metals) but still throwing some errors. Could someone help me to get an idea on how to parametrize molecules like cisplatin or related?
PD: I'm using VMD and NAMD, charmm-36 when is need and to generate cisplatin molecule I use avogrado.
Force field parameters for cisplatin can be found in the literature. The paper below is unlikely the only one out there:
Article Monte Carlo Simulation of Cisplatin Molecule in Aqueous Solution
Working with heavy metals using classical forcefields is tricky. As said before, you should generate parameters for your molecule by QM calculations or take appropriate parameters from the literature.
On the other hand, you should consider a QM/MM approach, applying the QM theory around your cisplatin molecule using appropriated basis sets. Look:
Preprint Characterization of Cisplatin/Membrane Interactions by QM/MM...
Thanks for helping. Force Fields parameters for cisplatin it really can be found in literature. If someone need helps with that, theses papers can be of help :
Article Monte Carlo Simulation of Cisplatin Molecule in Aqueous Solution
(as said Martin Klvana )Article Empirical force field for cisplatin based on quantum dynamic...
(From the same authors than article before, in this one you can found gromacs parameters for Cisplatin ... in a file)Article Developing multisite empirical force field models for Pt(II)...
Article Chemically Modified Carbon Nanohorns as Nanovectors of the C...
Those are relevant literature to obtain methodology on how parameterized Cisplatin molecule. Thanks to Martin Klvana and Edward Francisco Méndez Otálvaro for helping.
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