I also noticed that your parm99.dat is heavily modified compared to the
standard one. I would suggest using an actual parm99.dat from the Amber
distribution and see if that helps.
On Tue, Oct 8, 2019 at 2:00 PM Dawid das <addiw7.googlemail.com> wrote:
> Dear Carlos,
>
> Thank you for letting me know. It was from one of my previous test runs.
>
> I attach a correct log.
>
> Best wishes,
> Dawid
>
> wt., 8 paź 2019 o 19:33 Carlos Simmerling <carlos.simmerling.gmail.com>
> napisał(a):
>
> > for some reason in your leap.log file I see this:
> > #parm99 = loadamberparams parm99.dat
> >
> > it isn't that way in the files you sent though. do you know why this line
> > was commented? parm99.dat has the vdw parameters.
> >
> > On Tue, Oct 8, 2019 at 12:04 PM Dawid das <addiw7.googlemail.com> wrote:
> >
> > > Dear Amber Users,
> > >
> > > I am trying to generate topology and parameters files for a protein
> > > containing my own amino acid (unit).
> > >
> > > I attach my tleap.in, PDB and leap.log files together with some
> > parameter
> > > files I use as the input.
> > >
> > > The issue is that I get an error saying that vdW parameters are missing
> > > for virtually every atom even though I can see them correctly defined
> > > in leaprc.ff99SBildn and parm99.dat. What could be the problem?
> > >
> > > Best regards,
> > > Dawid Grabarek
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> > >
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> >
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Received on Tue Oct 08 2019 - 12:00:02 PDT
