[gmx-users] puzzling about adding H atoms

[wuxiao]

Dear gmx users,

  Through the manual, I learn of that both pdb2gmx and protonate can add H atoms according to the hdb files.  About it, I have some puzzles as follows:

  Are the two programs equivalent in adding H atoms? If it is yes, why bother to develop another program? It seems that protonate program can not generate partial atom charges, so after protonation, it still needs to do so.

  Thanks a lot ahead for any reply.

 

Best regards

Chaofu Wu

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