Hello:
I generate a ligand toplogy by ACPYPE with amber GAFF. However, I
found that in the ligandGMX.itp file, in the atomtypes section, the mass
and charge are all zero, like:
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
NT NT 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
however, in the atoms sections, I found:
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot
bond_type
26 NT 1 UKA N10 26 -0.719301 14.01000 ; qtot -7.758
I am a little bit confused for this. Does anybody have any idea for it?
thank you very much
best
Albert
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