[gmx-users] pdb2gmx + non-protein

[Alberto Imparato]

Hi All
I'm trying to obtain a topology file starting from a very simple .gro
file, using pdb2gmx .
My 2_dppc.gro file contains 2 DPPC molecules, each containing 50 atoms:

DPPC
  100
    1DPPC  C1  1   1.305  0.021  4.907   -0.4017   -0.1211   -0.18
    1DPPC  C2  2   1.345  0.856  4.733   -0.171   -0.6351   -0.2036
    1DPPC  C3  3   1.191  0.812  4.904   0.1336   0.3719   0.2801
    1DPPC  N4  4   1.244  0.919  4.819   -0.0492   -0.1049   -0.4439
    1DPPC  C5  5   1.131  0.985  4.751   -0.7172   -0.308   0.4587
    ....
    ....
    2DPPC  C1  51   1.305  0.021  0.093   -0.4017   -0.1211   -0.18
    2DPPC  C2  52   1.345  0.856  0.267   -0.171   -0.6351   -0.2036
    2DPPC  C3  53   1.191  0.812  0.096   0.1336   0.3719   0.2801
    2DPPC  N4  54   1.244  0.919  0.181   -0.0492   -0.1049   -0.4439
    2DPPC  C5  55   1.131  0.985  0.249   -0.7172   -0.308   0.4587
    ....
    ....

then I type "pdb2gmx -f 2_dppc.gro -p topol -o out.gro"

the topology file topol.top I obtain, looks like

#######################
#include "ffgmx.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
chargeB      massB
     1        CH3      1   DPPC     C1      1      0.124     15.035   ;
qtot 0.124
     2        CH3      1   DPPC     C2      1      0.124     15.035   ;
qtot 0.2
....
....
[ system ]
; Name
DPPC

[ molecules ]
; Compound        #mols
Protein             1
########################
WHY the 2 molecules are not recognized as DPPC molecules, but are treated
as 1 single Protein ???
The same happens when I first transform 2_dppc.gro to  2_dppc.pdb using
editconf and the process the latter file with pdb2gmx.
Thak you
Alberto