Dear all,
I'm trying use GROMACS to calculate binding free energy with MM-PBSA method
and do Computational Alanine Scanning. After run MD and obtain pdb files, I use
PYMOL to mutate one residue to Alanine to estimate the energy difference
between 2 structures. My issue is that I don't know how to generate topology
file (.top file) after mutation but not ignore hydrogen in initial file. If
using pdb2gmx command, it needs me ignore hydrogen and I think hydrogen after
using this command is not in the same place with hydrogen at first. This will
my my results unbelievable.
Can any ones help me ??
With the best regards;
Binh Khanh Mai
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