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

[David van der Spoel]

On 2013-06-08 17:28, Albert wrote:
> 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?
>
the ones in the atoms section are the ones that are used UNLESS they are 
not given, in which case the defaults are used.

> thank you very much
>
> best
> Albert


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se