Dear Dan,
I realized that fixatomorder changed the order of my input files.
Previously the all the glycans are at the end of the PDB file. After using
fixatomorder command, part of the glycans were moved to the middle (because
they connect to the residues of chain A, to be specific: resid 209 to 216).
That's why resid 209 to 216 are missing.
Thank you for your help.
Best regards,
Rui
On Mon, Oct 7, 2019 at 8:47 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I haven't received them. Could you maybe just extract 2 frames of the
> trajectory, then compress (gzip, bzip, etc) that and the topology file
> and send it? Unless the system is extremely large that should be
> fairly small.
>
> -Dan
>
> On Fri, Oct 4, 2019 at 1:32 PM Rui Chen <rchen6.ualberta.ca> wrote:
> >
> > Dear Dan,
> >
> > The files I sent to you were too big. I just want to check, have you
> > received my files?
> >
> > Best regards,
> > Rui
> >
> > On Thu, Oct 3, 2019 at 9:09 AM Rui Chen <rchen6.ualberta.ca> wrote:
> >
> > > Hi Dan,
> > >
> > > First of all I combined 6 trajectories into one single trajectory.
> Because
> > > CPPTRAJ complained the atom numbering is not sequential, I used
> > > fixatomorder command to solve the problem. Then I stripped all the
> waters
> > > and ions. In total I have 50000 frames, according to your suggestion, I
> > > re-generate the trajectory and the corresponding parameter file and
> > > attached them here, which only contain 20 frames. If you need other
> > > files, please let me know. Thank you. (Just to let you know,
> > > all_stripWI_sample.nc is the same as all_stripWI.nc, but with less
> frames.
> > > )
> > >
> > > Best regards,
> > > Rui
> > >
> > > On Thu, Oct 3, 2019 at 6:42 AM Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > >
> > >> 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
> > >> > >> > _______________________________________________
> > >> > >> > AMBER mailing list
> > >> > >> > AMBER.ambermd.org
> > >> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >>
> > >> > >> _______________________________________________
> > >> > >> AMBER mailing list
> > >> > >> AMBER.ambermd.org
> > >> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> > >>
> > >> > >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 07 2019 - 21:30:02 PDT
