[gmx-users] Overriding atom type.

[Alessandra Villa]

Hi,

On Wed, Dec 4, 2019 at 7:41 AM Yogesh Sharma <yogesh.rma13 at gmail.com> wrote:

> Hello Users,
> I was trying to run grompp  for a membrane protein - ligand dynamics. I am
> using  4 5 ligands together. Under grompp run I got error overriding
> atomtype HGP1. Came out two ligands were sharing similar naming in atomtype
> section. I wanted to ask is it harmless to change it manually are there any
> conventions for it ? following this are there any other changes  in
> topology file that i need to make?
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
>    CG2O6     6    12.0110      0.600     A    3.56359487256e-01
>  2.928800e-01
>     HGP1     1     1.0080      0.340     A    4.00013524445e-02
>  1.924640e-01
>    NG2S2     7    14.0070     -0.690     A    3.29632525712e-01
>  8.368000e-01
>    OG2D1     8    15.9994     -0.580     A    3.02905564168e-01
>  5.020800e-01 ;
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
>     HGP1     1     1.0080      0.500     A    4.00013524445e-02
>  1.924640e-01
>    OG311     8    15.9994     -0.500     A    3.14487247504e-01
>  8.037464e-01
>

[ atomtypes ] section in the top file is used to to customize your
non-bonded parameters
One can use this section to define new atom types, but this should take
place in line with the rest of the force field parameters.

In the above case I have noticed that non-bonded parameters (LJ) for HGP1
are identical in the two  [ atomtypes ],
and the atomic charge values are readed from the top file section [atoms].
If it is the case, you do not need to define it twice.

Best regards
Alessandra




Do you used custermized non-bonded parameters ?



> * thank you for your precious time.*
>
> * with  regards*
> *Yogesh Sharma*
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