Dear Dan,
My files are too big, I sent you once, however you couldn't receive them (I
already reduced the frames). I generated these two reorder files. Thank you
for your help.
Best regards,
Rui
On Thu, Oct 10, 2019 at 8:17 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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Received on Thu Oct 10 2019 - 16:00:02 PDT
