Hi,
I have successfully completed 1st phase of ab-initio surface docking using DNA-ligand model. But I’m stuck at generating .tbl files.
The tutorial says, use awk ‘$2>2000 && $2<4000’ AcrB-rifampicin-surface-full-contacts.lis |wc -l command to calculate top 10% most contacted residues.
But after executing $WDIR/contacts-statistics.csh cat file.nam, I got 2 new .lis files namely Acontacts.lis and Bcontacts.lis
My question is does AcrB-rifampicin-surface-full-contacts.lis(mentioned in tutorial) and Acontacts.lis(generated in my case) represents the same thing ?
Contents of Acontacts.lis:
9955 22 A
7595 10 A
7373 6 A
6923 7 A
6019 11 A
5644 8 A
5357 9 A
4638 21 A
2776 12 A
1119 5 A
810 20 A
293 19 A
264 15 A
235 16 A
150 4 A
113 18 A
96 14 A
55 17 A
37 13 A
36 3 A
33 1 A
2 2 A
Contents of Bcontacts.lis:
10000 0 B
Feeling a bit lost here. Please help me out.
Thank you
The answer to your question is: YES
In the tutorial the residue number of RFP is given as 2002 ( as used during .tbl file generation). In my case I have 22 residue DNA. So do I mention 23 as my ligand’s residue number ?
Another question is: Using your code I identified interacting residue number:
awk ‘$2>1 && $2<22’ Acontacts.lis | awk ‘{printf “%s,”, $2}’ . Gennerated active residue’s .tbl file, but for generation of passive residue’s tbl file the tutorial suggests that to submit the same residue numbers in passive field (given the http://haddock.science.uu.nl/services/GenTBL/). In doing so I got following output for passive .tbl:
! HADDOCK AIR restraints
! HADDOCK AIR restraints for 1st selection
!
! HADDOCK AIR restraints for 2nd selection
!
! HADDOCK AIR restraints for 3rd selection
!
! HADDOCK AIR restraints for 4th selection
!
! HADDOCK AIR restraints for 5th selection
!
! HADDOCK AIR restraints for 6th selection
!
Is this normal or I made some mistake ? It seems blank to me.
Please suggest.
Thank you.
Rear carefully the tutorial… In this case the ligand should be defined as active.
As for its number, it depends on what you have for it (i.e. which number is defined in your PDB). Does your ligand has residue number 23? If not then use the correct number.
In my pdb, the ligand’s residue number is 0 (zero). And so is in cluster.pdb (generated in docking runs). Given the scenario should I mention 0 for ligand residue number ? I’m little confused thinking if it is possible to have a residue number as 0. Will the program recognize ?
Even 0 should work! And if you are worried, simply change the residue number
Thank you for your comment.
I still have a query regarding the command i’m using: awk ‘$2>1 && $2<22’ Acontacts.lis | awk ‘{printf “%s,”, $2}’
What does ‘’$2>1 && $2<22" means here ? My target was to identify interacting residues between 1-22.
What does ‘’$2>1 && $2<22" means here ?
It means that awk will output only the lines where the 2nd column value is between 1 and 22.
| awk ‘{printf “%s,”, $2}’
And this part will output the 2nd column value sequentially (e.g. “1,5,12,13,21,”)
Thank you.
In the .tbl file generation server what does the “partner selection” box means ? Do I leave it as default value given there ?
You can leave it to the default if you only have two molecules, but if you are doing multi body docking, you might want to define more specific restraints between chains and then you should edit it accordingly.