Dear all
As part of a project, I am trying to parametrize a force field of PNA containing triplex-forming oligonucleotides. My first attempts to obtain the charges used REDDB tools with HF/6-31G and single conformation of dipeptides of the PNA, but the results were poor, at least considering the comparison of the predicted association constants with experiments (as there are no experimental structures in the PDB, this is the only benchmark that I can use). So I have decided to try a more elaborate parametrisation, using several conformations and also IpolQ as implemented in mdgx.
I am planning to follow a procedure inspired in the one published to get ff14ipq and ff15ipq force fields (although probably more modest). But I have not been able to understand the treatment of charged residues (some of the PNA are charged). Do I have to include an explicit countering in the simulations to get the average water distribution? Should the charge cloud of this counterion also be present in the single-point MP2 calculations?. Will mdgx take care of the charges when setting up the single-point calculation?
Another question… I will also need to parametrize some dihedrals (I will borrow angles and bonds from protein and RNA force fields… reparametrizing them is probably beyond what I can afford). Previously I created some models, excluding backbone atoms, for which I calculated charges using REDDB. Then I used these charges in the topologies for fitting the torsional terms in mdgx. This reduced computational time, and gives a simpler system to explore, since the torsional terms were not contained by, for example, steric interactions with the backbone atoms. I plan to follow the same approximation now, but I wonder if, for these models, I can simply use the vacuum MP2 energies (since I think that solv energy is not used for parametrising torsion terms in ff15ipq or ff14ipq).
Thanks
Luis
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Received on Mon Feb 08 2021 - 01:30:02 PST
