[gmx-users] why mass and charge is zero?
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jun 8 18:56:47 CEST 2013
On 2013-06-08 17:28, Albert wrote:
> 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?
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
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
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