Well, the only modifications I have introduced are regarding the new
parameters for a SYN unit
that I defined. They must be defined somewhere because SYN is an integral
part of my protein.
wt., 8 paź 2019 o 20:47 Carlos Simmerling <carlos.simmerling.gmail.com>
napisał(a):
> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 08 2019 - 12:00:03 PDT
