[gmx-users] why mass and charge is zero?

Albert mailmd2011 at gmail.com
Sat Jun 8 17:28:19 CEST 2013


  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   
     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


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