[gmx-users] Nucleic Acid in GROMOS54A7

[Mark Abraham]

Ok, so it sounds like you need to understand more about how your forcefield
works and what it names its residues, from its papers and from the files in
the forcefield implementation.

Mark

On Mon, 31 Jul 2017 12:19 Souparno Adhikary <souparnoa91 at gmail.com> wrote:

> DA is the Adenine residue. It goes fine with other forcefields like
> CHARMM27 and AMBER99 SBILDN. In my knowledge, there's no problem in the
> parameters.
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Mon, Jul 31, 2017 at 3:43 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > What is DA, and from your background knowledge of this force field, does
> it
> > have suitable parameters or topologies for DA?
> >
> > Mark
> >
> > On Mon, 31 Jul 2017 11:02 Souparno Adhikary <souparnoa91 at gmail.com>
> wrote:
> >
> > > Hi all,
> > >
> > > I was trying to simulate a protein-DNA complex using gromos54a7
> > forcefield.
> > > The error comes as,
> > >
> > > Fatal error:
> > > Residue 'DA' not found in residue topology database
> > >
> > > Clearly, it is not finding the DA residue in its database. How can I
> > solve
> > > this?
> > >
> > > Thanks,
> > >
> > > Souparno Adhikary,
> > > CHPC Lab,
> > > Department of Microbiology,
> > > University of Calcutta.
> > > --
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