Hi,
On Wed, Oct 2, 2019 at 6:18 PM Rui Chen <rchen6.ualberta.ca> wrote:
> 1. No matter I specify the residue numbers (1-416, which is only the
> protein) or I don't specify the residue numbers. The output I got from
> CPPTRAJ is weird, the residues 209 to 216 (also protein) are always
> missing. Is the script correct?
I would need the files you used to try to reproduce this issue. I
wouldnt need the whole trajectory, 5-10 frames would suffice.
> 2. If I want to perform an RMS fit to the first structure prior to the
> calculation, is "rms first" the correct command?
'rms first' will fit all atoms to the first frame. If you have solvent
this is not what you want - you'll want to specify the atoms you want
to use as a reference frame (typically your biggest solute molecule,
but could be just a region of the molecule).
> 3. Usually, fit to the average structure or the first structure?
You can do either. Personally I think a fit to the average structure
gives the best behavior.
-Dan
>
> Looking forward to your feedback, thank you.
>
> parm all_stripWI.prmtop
> trajin all_stripWI.nc
> #rms first
> atomicfluct out rmsf_bb_dimer_try.dat .C,CA,N byres
> go
> quit
>
> Best regards,
> Rui
>
> On Wed, Oct 2, 2019 at 8:41 AM Rui Chen <rchen6.ualberta.ca> wrote:
>
> > 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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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >>
> >
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Received on Thu Oct 03 2019 - 06:00:05 PDT
