this isn't related to the specific error you're getting, but more a general
comment.
it looks like you're trying to do something that's quite difficult (build
cellulose or lignin simulations).
Have you looked at the literature to see if this has been done before? For
example, the group at NREL has papers on that, and they are quite
experienced with Amber. Have you tried following the protocols they report
in their papers? Maybe asking for inputs would help. It seems like nobody
here has the level of expertise with building a cellulose crystal, and it's
not really a technical question so many people that might be able to help
won't be reading this email list. I would suggest finding similar papers,
and contacting the authors using the corresponding author email addresses
that are provided for this purpose.
On Mon, Feb 1, 2021 at 5:27 PM Pinky Mazumder <pmazumder67.gmail.com> wrote:
> Thank you very much for your response.
>
> . I increased the cell dimension. This did not work.
> I think the chamber tool is not generating the (.prmtop) properly.
>
> Is there any other way to make the (.pdb) file compatible with AMBER (
> means AMBER can recognize the residue)?
>
> I tried with the antechamber too using gaff2, but it also failed to
> generate the force field.
>
> Any help would be appreciated.
>
> Thank you!
>
> Regards,
> Pinky
>
> On Mon, Feb 1, 2021 at 4:26 PM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
>
> > Thank you very much. I increased the cell dimension. This does not work.
> > I think the chamber tool is not generating the (.prmtop) properly.
> >
> > Is there any other way to make the (.pdb) file compatible with AMBER (
> > means AMBER can recognize the residue)?
> >
> > I tried with the antechamber too using gaff2, but it also failed to
> > generate the force field.
> >
> > Any help would be appreciated.
> >
> > Thank you!
> >
> > Regards,
> > Pinky
> >
> >
> > On Thu, Jan 28, 2021 at 3:00 PM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Thu, Jan 28, 2021, Pinky Mazumder wrote:
> >> >> Common name cellulose
> >> >> Formula C12 H14 O10
> >> >> a 7.784 ± 0.008 Å
> >> >> b 8.201 ± 0.008 Å
> >> >> c 10.38 ± 0.01 Å
> >> >> My unit cell dimension is a=7,78, b=8.2, c=10.38. alpha=beta=90
> degree,
> >> >> gamma=96.5degree.
> >>
> >> Look at the bottom of the inpcrd file, which shows the real unit cell
> >> parameters:
> >>
> >> 17.1280000 36.8290000 43.5600000 90.0000000 90.0000000
> 90.0000000
> >>
> >> The "x" direction is only 17.1 Å, which is too small for Amber. If you
> >> need
> >> a periodic system, you need have more unit cellts in that direction.
> >>
> >> ....dac
> >>
> >>
> >
> > --
> > Pinky Mazumder
> > PhD Student
> > University of Alabama
> > USA
> >
>
>
> --
> Pinky Mazumder
> PhD Student
> University of Alabama
> USA
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Received on Mon Feb 01 2021 - 15:30:02 PST
