Thank Dr. Roe
My first part regarding the script. should it be saved as python script?
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
