Hi Daniel,
Very sorry for bothering you but something is surely not correct in my
input. I used your suggestion and wrote my input as
trajin combined.nc
hbond H1 series .N,H,C,O nointramol out hb.dat dist 3.5 avgout avg.dat
run
writedata solutehb.dat H1[solutehb]
runanalysis lifetime H1[solutehb.dat] out life.dat
However I get only two output files hb.dat and avg.dat. I dont get the
solutehb.dat and the life.dat as specified in one of the earlier
emails on the reflector list. Is something wrong here?
when I checked my log file I get the dataset written in the file. it ends with
DATAFILE OUTPUT:
hb.dat: H1[UU]
hb.dat: Writing 25011 frames.
[writedata solutehb.dat H1[solutehb]]
hb.dat: Writing 25011 frames.
[runanalysis lifetime H1[solutehb.dat] out life.dat]
But the life.dat file is not output. Again is something wrong here?
Also I notice that when I run the keyword "series", I miss my ligand
interactions. without it I could get some interactions.
I am pasting below the email from the reflector for reference. I have
updated and compiled my tools now to AmberTools13.
..........................
parm input.parm7
>> trajin input.nc
>> hbond HB out hbond.dat .N,C,H,O series avgout hbavg.dat printatomnum
>> run
>> write solutehb.dat HB[solutehb]
>>
>> This runs the Hbond command looking for hydrogen bonds in the given mask
>> selection (in this case just some protein backbone atoms). This will
>> generate 3 files: hbond.dat will have the total # solute-solute hbonds,
>> hbavg.dat will have the average occupancies etc for each hbond seen, and
>> solutehb.dat will have the raw occupancy vs time for each hbond (in
>> columns). The 'printatomnum' command will print the atom number for each
>> hbond in hbavg.dat. You can obtain grace or gnuplot style output for
>> hbond.dat/solutehb.dat by changing the extension to .agr/.gnu respectively.
>>
>> Hope this helps,
>>
>> -Dan
PS - You can also run lifetime analysis on the data generated by adding
> something like this after the 'run' command:
>
> runanalysis lifetime HB[solutehb] out lifehb.dat
..........................................
Thank you for all the prompt replies that I am getting
Ayesha
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Received on Thu Feb 19 2015 - 02:30:02 PST
