[gmx-users] .hdb---file in gromacs

Debashis Sahu debashis.sahu87 at gmail.com
Mon Jul 23 20:47:56 CEST 2012

Dear all user,
                  I'm a gromacs beginner and have a quick question.
Can anyone tell me about the .hdb file description, e.g. '8' indictes
no.of kind of hydrogen, ARG is residue name, after that 1st column
indicates the no. of hydrogens for each type but 2nd column's
indication is not clear to me. And also which basis the atom type are
mentioned in .hdb file. Here, I given the part of .hdb file for ARG
Please help me

ARG     8
1      1     H          N          -C           CA
1      5     HA       CA         N            C              CB
2      6     HB       CB         CG         CA
2      6     HG      CG         CD          CB
2      6     HD      CD          NE         CG
1      1     HE      NE          CD         CZ
2      3     HH1    NH1        CZ          NE
2      3     HH2    NH2        CZ          NE


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