Golshad Ghojoghi

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Questions related from Golshad Ghojoghi

FFParam: When optimizing partial charges, what can be done about water molecules clashing with the parent structure?

I am trying to parameterize a small compound (a non-standard backbone amino acid) using FFParam package. In the partial charge optimization stage, some of the placed water molecules clash with the...

08 February 2023 9,102 0 View

Does CHARMM-GUI input generator have any option to make topology with virtual sites?

I am trying to simulate a glycoprotein and generated GROMACS input files using CHARMM-GUI Input Generator (Glycan Reader). My molecule is large and I want to use a 4fs time step for the...

01 December 2022 3,516 0 View