Yes, it works when I don't have SYN and I use original files.
I must have messed something up while adding SYN definition.
Thank you for guiding me!
Best regards,
Dawid Grabarek
wt., 8 paź 2019 o 21:01 Carlos Simmerling <carlos.simmerling.gmail.com>
napisał(a):
> I think it's safest to put extra parameters into a new frcmod file instead
> of modifying the original.
> does it work when you don't have the SYN? you'll need to debug whether the
> problem is from the modifications or from some other issue.
>
> On Tue, Oct 8, 2019 at 2:58 PM Dawid das <addiw7.googlemail.com> wrote:
>
> > 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
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Received on Wed Oct 09 2019 - 02:00:02 PDT
