Many thanks, I will try it on cpptraj console.
Liyang
2017-03-01 8:13 GMT-08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Tue, Feb 28, 2017 at 1:59 PM, Liyang Zhu <liyangzhu.lbl.gov> wrote:
> >
> > (1) can we output non-nativecontact explicitly as the native.dat ?
>
> Yes, with the current GitHub version there are several new options for
> saving non-native contact info:
>
> [savenonnative [seriesnnout <file>] [nncontactpdb <file>]]
>
> They work just like their 'native' equivalents.
>
> > (2) why we need a reference frame?
>
> The 'nativecontacts' command was originally intended to track
> so-called "native" contacts, i.e. contacts that are present in some
> reference structure (e.g. X-ray crystal etc), hence the need for a
> reference.
>
> > Following above question, may be I need the last frame as reference, so I
> > trajout the lastframe.pdb, but it complaints not found the file. The
> > following are the input and error information.
> >
> > trajin reimagedprod.mdcrd
> > nativecontacts :MET.M1 :LIG.O1 byresidue resout res.dat out abc.dat
> distance 3.5 ref lastframe.pdb series seriesout native.dat
> > Error: Reference 'lastframe.pdb' not found.
> > Error: Could not initialize action [nativecontacts]
>
> Did you previously load lastframe.pdb with a 'reference' command, e.g.
>
> reference lastframe.pdb
>
> > I also tried using refindex 2000, here 2000 is the number of last frame
> in
> > .mdcrd file, but it still not works.
>
> You need to use the reference command. To load the last frame in the
> trajectory file as a reference:
>
> reference reimagedprod.mdcrd lastframe
>
> to load frame 2000 as a reference:
>
> reference reimagedprod.mdcrd 2000
>
> Hope this helps,
>
> -Dan
>
> >
> > Thanks a lot,
> > Liyang
> >
> >
> > 2017-02-02 6:59 GMT-08:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >
> >> Hi,
> >>
> >> It's an interesting problem. I think that maybe the 'nativecontact'
> >> command where you specify M in one mask and all the LX ones in the
> >> other (and use 'series' keyword to get the time series) might do what
> >> you want. Check the manual for details. Let me know if you have
> >> further questions.
> >>
> >> -Dan
> >>
> >> On Tue, Jan 31, 2017 at 3:32 PM, Liyang Zhu <liyangzhu.lbl.gov> wrote:
> >> > Dear all,
> >> >
> >> > In my system, there are 100 metal ions M, and 1000 ligands L, they
> >> > will form a series of complex, ML, ML2, ML3, in addition to free M and
> >> > L. I am wondering if there is a method to count the number of those
> >> > species, that is how many are the M, L, ML, ML2 and ML3.
> >> >
> >> > I though chechoverlap might work, but this command is not aimed to do
> >> > this task, it will report all the atoms in the range shorter than
> >> > coordination bond M-O(L), thus may be not easy to use. Does anyone
> >> > have a possible way to count the number?
> >> >
> >> > Thanks a lot,
> >> > Liyang
> >> >
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> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe
> >> Laboratory of Computational Biology
> >> National Institutes of Health, NHLBI
> >> 5635 Fishers Ln, Rm T900
> >> Rockville MD, 20852
> >> https://www.lobos.nih.gov/lcb
> >>
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>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Wed Mar 01 2017 - 18:30:02 PST
