[gmx-users] Problem with pdb2gmx in gromacs 4.5.3

[Tomy van Batis]

Dear Gromacs users

I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I
looked up the mailing list but I can't find something similar.

I have in a .pdb file a crystalline substrate consisting of Si particles.

By running in previous gromacs version (i.e. gromacs 3.3) :

*pdb2gmx -f name.pdb -p topol.top -o output.gro
*
I get the following result for the *topol.top *file*:*

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1         SI      1    ZZZ     D1      1          0      28.08   ; qtot
0
     2         SI      1    ZZZ     D2      2          0      28.08   ; qtot
0
     3         SI      1    ZZZ     D3      3          0      28.08   ; qtot
0
     4         SI      1    ZZZ     D4      4          0      28.08   ; qtot
0
     5         SI      1    ZZZ     D5      5          0      28.08   ; qtot
0
etc

which of course is normal, but by doing the same in gromacs 4.5.3,
the *topol.top
*file* *is the following:

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
; residue   1 ZZZ rtp ZZZ  q  0.0
     1         SI      1    ZZZ     D1      1          0      28.08   ; qtot
0
     2          O      1    ZZZ     D2      2          0 1.48594e-41   ;
qtot 0
     3          O      1    ZZZ     D3      3          0 1.48594e-41   ;
qtot 0
     4          O      1    ZZZ     D4      4          0 1.48594e-41   ;
qtot 0
     5          O      1    ZZZ     D5      5          0 1.48594e-41   ;
qtot 0
etc

I have no idea where these O come from.

Did anyone have similar problems?

Best regards, Chrysostomos
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