Hello, I want to make pH dependent simulation of dimer, trimer and pentamer structure of peptide. How to make it using AMBER or GROMACS?
Can I use H++ server for oligomers?
or
How to set manually. Do you have any suggestion?
Best regards,
Batsaikhan,
You can use H++, PropKa, etc. on your peptide to figure out its pKa values, though it could be complex to get it right. pKa depends on the microenvironment, so unless your peptide has some distinctive fold to it, the pKa values will not vary much from their canonical values.
Dear Mijiddorj, as Justin noted, first you have to find out in what ionization state are the amino acids of your complex at each pH your are going to run the simulations.Then run the simulations with the pH sensitive amino acids in the corresponding ionization state.
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