GROMACS version: 5.1.4
GROMACS modification: Yes/No
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Hi,
I want to run a MD simulation of a small DNA fragment that contains an unnatural base pair using CHARMM36 forcefield. I am having problems generating the parameters for the unnatural nucleotide, I even tried the solution builder in CHARMM-GUI (There is no similar molecule in the CSML library), but there also I got errors. So please can anyone tell me how to generate the parameters or if there is a general way to carry out these kinds of simulations, then please inform me.
Thank you in advance
Rick