[gmx-users] Query regarding protein topology constructed using -vsite hydrogen option.

[Abhishek Acharya]

Dear Gromacs Users,

I am trying to simulate a protein ligand complex and since the system is
quite large, thought to use virtual sites implementation for all hydrogen
atoms. I have generated a topology for the protein chain using pdb2gms
-vsite hydrogen option. But, I notice that the protein topology file
contains almost all the bonds, angle and dihedral parameters involving the
dummy atoms.

>From "Feenstra, Hess and Berendsen (1999) J Comput Chem", I understand that
all bonds to dummy atoms must be removed. Similarly, all angles involving
two or three dummy atoms should be excluded; same with dihedrals containing
at least one dummy atom.

Is this a mistake in the topology generated by pdb2gmx or am I missing
something?

Relevant sections from the topology file:

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
; residue   1 ASP rtp NASP q  0.0
     1       MNH3      1    ASP    MN1      1          0      8.517   ;
qtot 0
     2       MNH3      1    ASP    MN2      1          0      8.517   ;
qtot 0
     3         N3      1    ASP      N      1     0.0782          0   ;
qtot 0.0782
     4          H      1    ASP     H1      2       0.22          0   ;
qtot 0.2982
     5          H      1    ASP     H2      3       0.22          0   ;
qtot 0.5182
     6          H      1    ASP     H3      4       0.22          0   ;
qtot 0.7382
     7         CT      1    ASP     CA      5     0.0292     13.018   ;
qtot 0.7674
     8         HP      1    ASP     HA      6     0.1141          0   ;
qtot 0.8815
     9         CT      1    ASP     CB      7    -0.0235     14.026   ;
qtot 0.858
    10         HC      1    ASP    HB1      8    -0.0169          0   ;
qtot 0.8411
    11         HC      1    ASP    HB2      9    -0.0169          0   ;
qtot 0.8242
    12          C      1    ASP     CG     10     0.8194      12.01   ;
qtot 1.644
    13         O2      1    ASP    OD1     11    -0.8084         16   ;
qtot 0.8352
    14         O2      1    ASP    OD2     12    -0.8084         16   ;
qtot 0.0268
    15          C      1    ASP      C     13     0.5621      12.01   ;
qtot 0.5889
    16          O      1    ASP      O     14    -0.5889         16   ;
qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    3     4     1
    3     5     1
    3     6     1
    3     7     1
    7     8     1
    7     9     1
    7    15     1
    9    10     1
    9    11     1
    9    12     1
   12    13     1
   12    14     1
   15    16     1
   15    17     1

[ angles ]
;  ai    aj    ak funct            c0            c1
c2            c3
    4     3     5     1
    4     3     6     1
    4     3     7     1
    5     3     6     1
    5     3     7     1
    6     3     7     1
    3     7     8     1
    3     7     9     1
    3     7    15     1
    8     7     9     1
    8     7    15     1
    9     7    15     1
    7     9    10     1
    7     9    11     1
    7     9    12     1
   10     9    11     1
   10     9    12     1
   11     9    12     1
    9    12    13     1
    9    12    14     1
   13    12    14     1
    7    15    16     1
    7    15    17     1
   16    15    17     1

Thanks in advance.

Abhishek