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
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Received on Mon Oct 07 2019 - 08:00:02 PDT
