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

[Abhishek Acharya]

A little closer reading of the manual, I encountered a note in Topology
section, saying that the preprocessor removes the constant bonded
interactions between virtual sites and normal atoms; the bonded
interactions are required for generation of exclusions.

Thank you.
Abhishek

On Fri, Nov 23, 2018 at 7:43 PM Abhishek Acharya <abhi117acharya at gmail.com>
wrote:

> 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
>