[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Mijiddorj B]

Dear Justin,

As you suggested, I generated the charmm36 parameter using cgenff for
single unit with two capping groups. After that, I created 3 residues based
on the parameter of cgenff including N-ter side, Middle, and C-ter side
residues. However, the net charges of these residues are not equal to zero
as -0.002, -0.004, and -0.002, respectively.

1. How can I adjust the charge of these residue?
2. Is it possible to run simulation ignoring the grompp comments?

Best regards,
Mijiddorj

On 11/20/19 8:51 PM, Mijiddorj B wrote:
> > Dear Prof. Justin,
> >
> > Thank you very much for your reply. I would like to use charmm27 because
> my
> > system contains a surface model, which were parametrized by INTERFACE
> Force
> > Field and compatible with charmm27. The polymer parameters of charmm27
> were
>
> AFAIK there's no reason to believe you have to use CHARMM27; INTERFACE
> is generally compatible with CHARMM, which has a linear development
> history so you should be able to combine it with any CHARMM potential.
>
> > generated by swissparam, and the server renamed the atomtypes. I would
> like
> > to assign those parameters with original charmm27. If possible, I would
> > like to use original charmm27 parameters instead of the values of
> > swissparam. I used charmm36 atomtypes for clarification.
> > I do not know the atom type of the nitrogen which connected with three
> > carbons.
>
> NG301. I still think it's best if you simply parametrize your monomer
> units with CGenFF and use its parameters unless there are major penalties.
>
> -Justin
>
>