[gmx-users] why mass and charge is zero?
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 0.0 0.0 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] why mass and charge is zero?
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 0.0 0.0 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. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] why mass and charge is zero?
On 06/08/2013 06:56 PM, David van der Spoel wrote: the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. IC. thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
