Date: Wed, 9 Oct 2019 16:41:30 -0600
Dear Dan,
As you can see I got the following errors. I already used the fixatomorder
command, as long as I use the output trajectory generated by trajout
command and the corresponding topology file, I won't have a problem and I
don't need to worry about the errors, am I correct?
Another question is that my model is a glycosylated homodimer, should I
center only the protein or everything(protein + glycans)? Do you have any
suggestions about how to choose the residues to center?
Best regards,
Rui
[image: Screen Shot 2019-10-09 at 4.19.01 PM.png]
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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>
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