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 - 08:30:03 PST
