Hi,
On Mon, May 3, 2021 at 9:30 AM Ayesha Fatima <ayeshafatima.69.gmail.com> wrote:
> My first part regarding the script. should it be saved as python script?
You mean your parmed script? I think maybe you need the '-i' command
line flag, i.e. just execute it like 'parmed -i parmd.in`.
-Dan
> Thank you
>
> On Mon, May 3, 2021 at 3:58 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Sun, May 2, 2021 at 12:32 PM Ayesha Fatima <ayeshafatima.69.gmail.com>
> > wrote:
> > >
> > > I also tried using cpptraj but it also throws me the error of
> > >
> > > *Molecule NLU1 is not defined in gromacs topology.*
> >
> > First, I really don't recommend using cpptraj to do topology
> > conversions. Cpptraj is really only intended for trajectory/data
> > analysis; it has *not* been vetted at all for converting parameters
> > between different formats.
> >
> > Second, by default cpptraj will look for gromacs topology data (that
> > is not in the same directory) in the directory defined by the GMXDATA
> > environment variable; specifically, it expects things to be in the
> > "$GMXDATA/top" directory. I just realized this is not documented
> > (oops).
> >
> > Hope this helps,
> >
> > -Dan
> >
> > >
> > > NLU1 is the ligand
> > >
> > > is the ligand.itp required or gro file required
> > >
> > > thanks you
> > >
> > > Ayesha Fatima
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Received on Mon May 03 2021 - 07:00:03 PDT
