Re: [AMBER] Methods to count the different species

From: Liyang Zhu <>
Date: Tue, 28 Feb 2017 10:59:53 -0800

Dear Roe,

Sorry for late reply. Recently I come back to this question, and tried your
suggestion. nativecontacts works fine, and it can count just one particular
frame which is I need, by using trajin XXX.pdb, instead of trajin

I have several minor questions want to known.

(1) can we output non-nativecontact explicitly as the native.dat ?
In my system, the nativecontact is 1 or 2 if use the first frame as
reference, and non-nativecontact will increase with frames, so I want a
detailed nonativecontact infomation like "series seriesout native.dat"
shown. And the output may be mess in this case, since the nonativecontact
is very large.

(2) why we need a reference frame?

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]

I also tried using refindex 2000, here 2000 is the number of last frame in
.mdcrd file, but it still not works.

Thanks a lot,

2017-02-02 6:59 GMT-08:00 Daniel Roe <>:

> 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 <> 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
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
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Received on Tue Feb 28 2017 - 11:30:02 PST
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