I don't understand if you're having an issue here or not. Based on the
screenshot (by the way, sending actual text is almost always better
than a screenshot) you posted you should have ended up with 2 files
after that run:
reorder.solvated_g1I8L.prmtop (reordered topology)
all_reorder.nc (reordered trajectory)
Those are the files you would use for all future analysis.
> should I center only the protein or everything(protein + glycans)?
General advice for using 'autoimage' is to choose as your "anchor"
something that you want centered in the unit cell. Without seeing your
system I can't make a more specific recommendation than that.
-Dan
On Wed, Oct 9, 2019 at 6:41 PM Rui Chen <rchen6.ualberta.ca> wrote:
>
> 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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> >
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Received on Thu Oct 10 2019 - 07:30:03 PDT
