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When I prepare my protein with Process it works but I obtain the message :

Unknown protein atom : HT1 VAL10 16

Unknown protein atom : HT2 VAL10 17

Unknown protein atom : HT3 VAL10 18

This residue is N-terminal and these 3 Hydrogens are on the N


Solution:

The atom names need to comply with the IUPAC strandards. Therefore, the correct naming for the terminal nitrogen's hydrogens are H1, H2 and H3.  Depending on the software you use to add the hydrogens, you may not have a perfectly compliant mol2 format.

 
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