I have already tried AMBER and other force fields. The problem is with topology file creation. As there is no crystal structure or even a similar structure. So, I have to predict the structure using Ab initio modelling. In AMBER, the H++ server cannot process the model structure. Is there any alternative method for creating a topology file?
Alisa Gorislav
Here is a similar topic from GROMACS forum so maybe you would find it useful - https://gromacs.bioexcel.eu/t/metal-ion-moves-away-from-the-enzyme-during-the-simulation/5036/2
Also maybe there is a sense to find paper contains similar MD protocols like this - Article Mg2+ vs Ca2+ bound active site of group II intron– A MD study
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