Thank you
On Mon, 3 May 2021, 4:41 pm Daniel Roe, <daniel.r.roe.gmail.com> wrote:
> 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
