Yes, I am starting from scratch now.
Best regards,
DG
śr., 9 paź 2019 o 11:04 Bill Ross <ross.cgl.ucsf.edu> napisał(a):
> Apparently you lack superhuman memory and make mistakes too, not unlike
> the rest of us, so I suggest you start over from scratch, copy fresh
> canonical files, and create your own custom ones to debug. You may have
> trashed real data, since you've been changing canonical files and don't
> know what you're doing. If not yourself, think of the poor postdoc in a
> concentration camp 10 years from now who is forced to replicate your
> flawed results.
>
> Bill
>
> On 10/9/19 1:54 AM, Dawid das wrote:
> > 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 - 02:30:02 PDT
