Hi Daniel,
Thank you for your suggestions.
>> trajin 05_Prod_450-500ns_completehow_nowat.nc
>> average avg.nc
>> reference avg.nc [ref1]
>
> Note that the above input may not work as you expect.
I had already noticed this and had overcome it by creating a separate cpptraj.in file that did the average first, I forgot to add that to the email. Thanks for letting me know this!
> If you know for a fact that for example the CA of residues ~50 and ~400 are
> within 5.4 Ang. throughout the simulation then there may be a bug.
I do not know this so I do not think there is a bug. I just made the comment because in the manual it says that the map flag creates a 2D map normalized to 1.0.
> essentially the map is always symmetric. This is done because non-native contacts, which are
> by definition unknown a priori, are also included (they subtract from
> the map instead of add like native contacts).
I’m afraid I haven’t understood this part. I am only trying to record the distances between each pair of my two masks and monitor how many times during the simulation it goes below a certain threshold. How are non-native contacts defined?
So basically, there is no way for nativecontacts to do exactly what I want? The closest would be to perform this:
distance contact1 :
1.CA :
249.CA
filter contact1 min 0.0 max 5.4 out contact1.dat
outtraj maxmin.nc
run
And then check if there are contacts in the contact1.dat file with a simple grep command. The problem is that I have 33810 of these distances to evaluate for a 161 aa chain vs. a 210 aa chain. I’ve tried other options of cpptraj but I’m struggling to achieve the graph I want to have.
I’m looking forward to the improvements in the nativecontacts function.
Thanks again for the comments,
Juan
>
> Hi,
>
> I have some comments on your input script below, but first let me
> address your concerns regarding the 'nativecontacts' action.
>
> On Wed, Jan 28, 2015 at 6:02 AM, Juan Eiros Zamora
> <j.eiros-zamora14.imperial.ac.uk> wrote:
>> In particular, I am specifying as <mask2> the CA of one of the subunits
>> (:1-161.CA), and <mask1> as the CA of the other subunit I am interested in
>> (:249-458.CA). I am also enabling the results to be written as a contacts
>> map in 2D with the map flag. Nevertheless, the results I am getting from
>> this map file are not normalised from 0 to 1, and the interactions are
>> recorded between from :1 to :458, thus obtaining a symmetrical map.
>
> Unless your distance cutoff is actually satisfied throughout the
> entire simulation, you will not obtain a contact value of 1.0. If you
> know for a fact that for example the CA of residues ~50 and ~400 are
> within 5.4 Ang. throughout the simulation then there may be a bug.
> Currently the matrix dimensions are determined by the max and minimum
> values (atoms or residues) in either mask, so essentially the map is
> always symmetric. This is done because non-native contacts, which are
> by definition unknown a priori, are also included (they subtract from
> the map instead of add like native contacts).
>
> The 'nativecontacts' action is fairly new, and not quite polished, so
> feedback like this is extremely appreciated. I've been working on
> several enhancements to this action to make it more user-friendly
> (ability to create a time-series for native contacts, splitting the
> single map into separate native and non-native contact maps etc) which
> will be available in the next cpptraj release.
>
> Based on the output from 'nativecontacts', you may want to take a look
> at the 'filter' or 'outtraj' (with 'maxmin' keyword) to select frames
> which match your criterion. For example, say that you know from
> 'nativecontacts' that residues 50 and 400 and 10 and 300 are important
> contacts. You could use the following input to obtain an average
> structure of frames where both contacts are formed:
>
> parm nowatcompletehow.prmtop
> trajin 05_Prod_000-050ns_completehow_nowat.nc
> distance contact1 :50.CA :400.CA
> distance contact2 :10.CA :300.CA
> filter contact1 min 0.0 max 5.4
> filter contact2 min 0.0 max 5.4
> average contacts.rst7
>
>> trajin 05_Prod_450-500ns_completehow_nowat.nc
>> average avg.nc
>> reference avg.nc [ref1]
>
> Note that the above input may not work as you expect. The 'average'
> command requests that an average structure be created, but until the
> run is finished that file is not present, so the subsequent
> 'reference' command will try to read the 'avg.nc' file that is there,
> not the one being generated by the 'average' command. Better input
> would be like so:
>
> parm nowatcompletehow.prmtop
> trajin 05_Prod_000-050ns_completehow_nowat.nc
> average avg.nc
> run
> reference avg.nc [ref1]
> nativecontacts :249-458.CA :1-161.CA distance 5.4 ref [ref1] byresidue \
> map mapout map2.dat
> run
>
> In this case the first 'run' will execute the 'average' command and
> create avg.nc, then the second 'run' command will execute the
> 'nativecontacts' command. The Action queue is cleared after every run
> but topologies/trajectories are not (to enable multiple passes like
> the above example). I've got some improvements in the works that will
> allow cpptraj to treat reference structures like data sets (so e.g.
> the 'average' action could generate a reference structure without
> having to write it and read it back in).
>
> Also, you may want to add an 'rms first' command before 'average' to
> remove global translational/rotational motion from your average
> structure.
>
> Hope this helps,
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu Jan 29 2015 - 09:00:02 PST
