Hi Dan,
We found a solution in the following link:
http://archive.ambermd.org/201604/0469.html, which parmed gave someone the
similar error.
"fixatomorder outprefix reorder" command helped me solve the problem, the
output trajectory was .nc (AMBER) format.
Best regards,
Rui
On Wed, Oct 2, 2019 at 7:32 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Oct 1, 2019 at 6:36 PM Rui Chen <rchen6.ualberta.ca> wrote:
> > I uploaded a parameter file into CPPTRAJ. I got the following errors. I
> > double checked the atom numbering is sequential. It seems like the
> problem
>
> It's not that atom numbering is sequential - it's that the atom range
> in the molecule is not completely contiguous. So something like this:
>
> Molecule 1: Atoms 1 2 3 4 10 11 12 13
> Molecule 2: Atoms 5 6 7 8 9
>
> Cpptraj (and I think other programs in Amber as well) operates on the
> assumption that molecules are completely contiguous (this is
> beneficial for a lot of reasons). When they aren't, cpptraj kicks back
> this error. I think parmed will give you a similar warning.
>
> > Just to let you know, this is a homodimer and the following mentioned
> atom
> > 6615 is the first atom of the glycans. I think the problem is the
> > glycan/protein interactions. I tried the four ways mentioned in the first
> > snapshot, none of them worked.
>
> Can you elaborate on *exactly* what you did and describe exactly why
> it didn't work? We need way more information to help.
>
> -Dan
>
> >
> > Could you please give me some clues? Looking forward to your reply.
> >
> > [image: Screen Shot 2019-10-01 at 3.45.59 PM.png]
> >
> > [image: Screen Shot 2019-10-01 at 3.47.01 PM.png]
> >
> > Best regards,
> > Rui
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 02 2019 - 08:00:02 PDT
