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 Fri Oct 04 2019 - 11:00:02 PDT
