I am able to run both ab initio calculations and MD simulation. However, I am relatively new to parameterising non-bonded interactions (transition metal in an active site supported by non-bonded interactions with histidine) in an MD forcefield (ran on Gromacs code) with data I have acquired from ab initio (DFT, Gaussian) calculations.
I understand that partial charges are required, but what other information will I need from Gaussian to complete my parameterisation of transition metal with histidine?
Many thanks
Normally, QM calculations are used to establish target data for MM force fields, so things like QM interaction energies or configurational energies are used as targets. The MM parameters are then tuned to give reasonable agreement with the QM results. Empirical refinement is often needed to strike a balance between in vacuo QM and condensed-phase MD applications. For which force field are you trying to develop parameters?
Hi,
I am thinking (currently reading up on) of parmeterising the AMBERFF99SB forcefield but running on Gromacs. But, this is mainly to fit in with the ethos of the group I work with who are heavily into AMBER. I understand that I would need to use tools such as MTK++ and Metal Center Parameter Builder. But I am unsure how this would fit in with Gromacs given that they tools *might* require the Amber Toolset.
I would consider switching/trying-out a forcefield which is designed for soluble proteins, came with the latest installment of gromacs and can be refined using DFT calculations.
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