Hi,
Just curious Wesley - have you tried the 'resseries' keyword of
'nativecontacts'? Does it not work the way you need? I'm interested
because it's relatively recent and any feedback I can use to improve
it would be helpful. Thanks,
-Dan
On Mon, Nov 20, 2017 at 8:25 PM, Wesley Michael Botello-Smith
<wmsmith.uci.edu> wrote:
> I think you can probably use the cpptraj 'nativecontacts' to accomplish
> this task (or at least generate the needed data to do so).
>
> eg:
> ----
> cpptraj systemTopology.parm7
> trajin trajectory.nc
> nativecontacts ':ligandResidNumbers' ':receptorResidNumbers' writecontacts
> residueContactInfo.dat
> go
> ---
> The file 'residueContactInfo.dat' would then be a 6 column file of the form:
>
> # Contact Nframes Frac. Avg Stdev
>
> You could then use the 'Frac' column to figure out what you need.
> This column would contain an entry for each atom in the first mask
> (:ligandResidNumbers) that was in contact with an atom in the second mask
> (:receptorResidNumbers) which corresponds to the percentage of frames for
> which the two atoms were in contact.
>
> If you need this by residue instead of by atom, you would need to use the
> 'series' and 'seriesout' options (see the amber manual) this gets you the
> breakdown of each atom for each frame.
> You would then need to summarize over both atoms and frames to get the per
> residue contact fraction.
>
> I've had to do something similar to this quite a few times recently so I
> wrote an R script to analyze the results.
> Assuming you name the series data file 'contactData.dat' then to do so in
> R, you could use the following:
> ------
> require(dplyr)
> require(tidyr)
> require(tibble)
> require(reshape2)
> require(Matrix)
>
> #load the data into an R data.frame
> testDat <- read.table("contactData.dat",header=TRUE,comment.char = "%")
>
> #format the data to be a 4 column format "FRAME X.RESID Y.RESID
> CONTACT_COUNT"
> #and compute the contact sums over each atom in a given X or Y RESID
> parsedData<-testDat %>%
> rename(FRAME=X.FRAME) %>%
> melt(id.vars=c("FRAME"),variable.name="CONTACT_PAIR",value.name="CONTACT_COUNT")
> %>%
> separate(CONTACT_PAIR,c("X","Y"),sep="_")%>%
> mutate(X=gsub("X[.]","",X),Y=gsub("^[.]","",Y))%>%
> separate(X,c("X.RESID","X.ATOM")) %>%
> separate(Y,c("Y.RESID","Y.ATOM")) %>%
> group_by(FRAME,X.RESID) %>%
> summarise(CONTACT_COUNT=sum(CONTACT_COUNT))
> parsedData%>%head
>
> #summarise over frames and ligand resids, assuming you used the second mask
> #to be your receptor ids when generating your series in cpptraj, this means
> that
> #Y.RESID will contain the residue id for each receptor residue of a given
> contact
> #you then need to take the average over all ligand RESIDs with which it had
> contact
> #this yields the 2 column format table "RESID CONTACT_FREQ"
> testSummary <- parsedData %>%
> group_by(Y.RESID) %>%
> summarise(CONTACT_FREQ=mean(CONTACT_COUNT>0))
> testSummary %>% head
>
> #write the data to an output file
> testSummary %>% write.table("ReceptorContactData.dat")
> ----
>
> hope that helps.
>
> On Wed, Nov 15, 2017 at 9:36 PM, anu chandra <anu80125.gmail.com> wrote:
>
>> Dear Amber users,
>>
>> I am working with protein-ligand system and there are ten residues lining
>> the binding pocket which have potential to interact with the ligand. Here,
>> I would like to calculate the percentage/fraction each of the ten residues
>> interact with ligand during the course of simulation (for e.g., how many
>> frames out of ,say, 100 frames have residue-1 interact with ligand). I
>> wonder if there is way I can do such calculation in CPPTRAJ.
>>
>> Any suggestion would be highly appreciated
>>
>>
>> Many thanks in advance
>> Anu
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 21 2017 - 06:00:03 PST
