[gmx-users] Question about "ffG43b1.rtp"

zjim fit_tone at 163.com
Thu Jan 13 13:05:53 CET 2005


When i was looking for "rtp data" of glucose in the ffG43b1.rtp. it seemed to have one.but i find that the number of O atom is not right as it should be six yet five in the file. otherwise, i was also confused to the atom type "+N" found
in [bonds] section and i couldn't find it in "ffG43b1.atp" and "ffG43b1nb.itp" file.
the "rtp data" of glucose in the ffG43b1.rtp showed as follow!
 [ GLCA ]
 [ atoms ]
   C1   CH1    0.400     0
   O5    OA   -0.360     0
   C5   CH1    0.160     0
   C6   CH2    0.150     1
   O6    OA   -0.548     1
   H6     H    0.398     1
   C2   CH1    0.150     2
   O2    OA   -0.548     2
   H2     H    0.398     2
   C3   CH1    0.150     3
   O3    OA   -0.548     3
   H3     H    0.398     3
   C4   CH1    0.160     4
   O4    OA   -0.360     4
 [ bonds ]
   C1    O5    gb_19
   C1    C2    gb_25
   O5    C5    gb_19
   C5    C6    gb_25
   C5    C4    gb_25
   C6    O6    gb_19
   O6    H6    gb_1 
   C2    O2    gb_19
   C2    C3    gb_25
   O2    H2    gb_1 
   C3    O3    gb_19
   C3    C4    gb_25
   O3    H3    gb_1 
   C4    O4    gb_19
   O4    +N    gb_19
 [ angles ]
;   ai    aj    ak  gromos type
 NH3*    C1    O5    ga_8 
 NH3*    C1    C2    ga_8 
   O5    C1    C2    ga_8 
   C1    O5    C5    ga_9 
   O5    C5    C6    ga_8 
   O5    C5    C4    ga_8 
   C6    C5    C4    ga_7 
   C5    C6    O6    ga_8 
   C6    O6    H6    ga_11
   C1    C2    O2    ga_8 
   C1    C2    C3    ga_7 
   O2    C2    C3    ga_8 
   C2    O2    H2    ga_11
   C2    C3    O3    ga_8 
   C2    C3    C4    ga_7 
   O3    C3    C4    ga_8 
   C3    O3    H3    ga_11
   C5    C4    C3    ga_7 
   C5    C4    O4    ga_8 
   C3    C4    O4    ga_8 
   C4    O4    +N    ga_9 
 [ impropers ]
;   ai    aj    ak    al  gromos type
   C1    O5  NH3*    C2    gi_2 
   C5    O5    C6    C4    gi_2 
   C2    O2    C3    C1    gi_2 
   C3    O3    C2    C4    gi_2 
   C4    C3    O4    C5    gi_2 
 [ dihedrals ]
;   ai    aj    ak    al  gromos type
   -C  NH3*    C1    C2    gd_14
 NH3*    C1    C2    C3    gd_17
 NH3*    C1    C2    C3    gd_7 
   O5    C1    C2    C3    gd_7 
   O5    C1    C2    O2    gd_8 
 NH3*    C1    C2    O2    gd_8 
   C1    C2    O2    H2    gd_12
   C1    C2    C3    C4    gd_17
   C1    C2    C3    O3    gd_7 
   O2    C2    C3    C4    gd_7 
   O2    C2    C3    O3    gd_8 
   C2    C3    O3    H3    gd_12
   C2    C3    C4    C5    gd_17
   C2    C3    C4    O4    gd_7 
   O3    C3    C4    C5    gd_7 
   O3    C3    C4    O4    gd_8 
   C2    C1    O5    C5    gd_14
   C1    O5    C5    C4    gd_14
   C4    C5    C6    O6    gd_17
   C4    C5    C6    O6    gd_7 
   O5    C5    C6    O6    gd_8 
   C5    C6    O6    H6    gd_12
   C6    C5    C4    C3    gd_17
   O5    C5    C4    C3    gd_7 
   C6    C5    C4    O4    gd_7 
   O5    C5    C4    O4    gd_8 
   C3    C4    O4    +N    gd_14

Is that right? 
Can somebody give an expaination?
thanks a lot

Shanghai Institute of Organic Chemistry
Computational Chemistry Lab
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