[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Sourav Ray]

Hello

Thanks for your answer, I presume pdb2gmx needs some force-field
definitions to work, anyway, can I assign charges selectively to certain
atom  number? Let me know if it is feasible, I searched the forums but
couldn't find anything specific.

Regards
Sourav

On Wed, May 25, 2016 at 2:48 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If you've already arranged your own termini, then you can choose "None"
> from the options pdb2gmx presents.
>
> Mark
>
> On Tue, May 24, 2016 at 11:15 PM Sourav Ray <souravray90 at gmail.com> wrote:
>
> > Hello
> >
> > I am trying to put selective charges on the termini, I am getting stuck
> at
> > the initial stage where I am supposed to mention the force-field needed.
> As
> > martini termini differ from conventional ones, I am unable to bypass NH3+
> > or COO- termini options at the start and end respectively as there is no
> > appropriate force-field option present there. Please let me know if
> anyone
> > has a workaround.
> >
> > Regards
> > Sourav
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