Carlos Javier Almeciga-Diaz

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Questions related from Carlos Javier Almeciga-Diaz

How to generate topology in gromacs for a peptide with an acetylated Lys?

I need to run a molecular dynamics simulation in gromacs with a peptide that has an acetylate Lys residue. This residue is not in topology database (GROMOS96 43a1 force field). How can I generate...

02 February 2017 9,961 3 View

How to calculate the RMSD for a part of a protein after MD in gromacs?

I did a MD simulation in gromacs for a protein and I would like to calculate the RMSD just for a part of the protein instead that for the whole protein. Any idea how to do that?

01 January 2017 5,983 7 View