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<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt; color: rgb(0, 0, 127);">Dear all,<br> 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.<br><div>Can any ones help me ??<br>With the best regards;<br>Binh Khanh Mai<br></div>
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