Re: [AMBER] Methods to count the different species

From: Daniel Roe <>
Date: Thu, 2 Feb 2017 09:59:17 -0500


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.


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 Thu Feb 02 2017 - 07:00:04 PST
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