Menu
▾
▴
1 Attachments
#12 no interaction with ligand and mol2
Hi
I want to prepare the ligand file. I followed the tutorial and read the paper. But after running the docking and opening mol2 file and the docking output, the ligand doesnt have any interaction with the structure. I was wondering why it is like that?
I read in the tutorial that we need to put the ligand in the cavity, is that correct? how and why we should do it? I appreciate if you help me with that.
I also attached my prm file.
Related
Discussion
Anonymous
I was wondering if anybody can hep me with this problem??
Hi Sam,
For what you explain, it looks like you wrongly defined the cavity. The sd
file you use for defining it should be placed in the binding site, or you
can define the cavity based on a set of coordinates. You can take a look at
the cavity to confirm that: you can see how to do it here
http://rdock.sourceforge.net/docking-in-3-steps/ (section 2).
We cant help with just the prm file, but please take a look and let me know!
Cheers,
Sergio
On Sat, 27 Jun 2020, 05:13 sam, sabm@users.sourceforge.net wrote:
Related
Tickets: #12
Hi Sergi,
Thank you for your reply. I defined the cavity. I have attached the outputs of running these commands:
rbcavity -r rdock.prm -was > rna_cavity.log
rbdock -r rdock.prm -p dock.prm -n 100 -i ligand.sd -o rna_docking_out > rna_docking_out.log
sdsort -n -f'SCORE' rna_docking_out.sd > 2qwy_docking_out_sorted.sd
sdrmsd ligand.sd 2qwy_docking_out_sorted.sd
But still getting the same results. I can tell after running rbcavity commands the caviy has been determinded in the log file. Please let me know what part is missing. I have tried different things in the past two weeks but it is still not fixed.
Many thanks
Hi Sam,
The program is working fine.
As I mentioned in the previously, please follow the instructions on section
2 of http://rdock.sourceforge.net/docking-in-3-steps/:
If you run rbcavity with the -d option: rbcavity -was -d -r <prmfile></prmfile>, it
will create a grd file that you can open in pymol and will help you
troubleshoot your problem.
The ligand you are using to define the docking site is not in contact with
the receptor, so all the docked poses will not interact with the receptor,
either.
You need to define the REF_MOL ligand.sd http://ligand.sd with a ligand.sd
http://ligand.sd file that is actually in the vicinity of the receptor,
so the definition of the docking site is correct and your docked poses will
then fall into that defined cavity.
Hope that helps,
Sergio
On Sat, 27 Jun 2020 at 10:46, sam sabm@users.sourceforge.net wrote:
Related
Tickets: #12
Hi sergio,
Thank you very much for your reply. You actually pointed out thr prolem. By visualizing I noticed my ligand is not defined in the vicinity of the receptor.
How should I put the ligand in the vicinity of receptor? or what software or method I should use to define that?
rbcavity -was -d -r <prmfile> will only creat a box around the ligand.
Please help me with that so I can proceed with my simulation. </prmfile>
Thanks a lot in advance.
Bests,
Sam
Hi Sam,
That's correct, glad you fount it out! It's up to you to choose a method to
define the cavity, but I would recommend pocket (
https://github.com/Discngine/fpocket) and then using the desired pocket
identified as a dummy ligand for rdock cavity definition.
Note also that you can use the "Two sphere method" to define the cavity
(section 5.1 in the documentation
http://rdock.sourceforge.net/wp-content/uploads/2015/08/rDock_User_Guide.pdf),
where you would only need the coordinates of the region you want to use as
docking site.
Good luck and happy docking!
Sergio
On Mon, 29 Jun 2020 at 12:17, sam sabm@users.sourceforge.net wrote:
Related
Tickets: #12
Hi Sergi,
I am using rdock for docking RNA-ligand, but with my HTVS ligand file, I am getting a Segmentation fault (I have splitted my files so split1.sd is one of them). I am not sure what is wrong with my input files and I would appreciate I you help me with it. I also used the DUD (ace) test files for my ligand database but still I am getting the same error. I appreciate it if you help me with this.
I am using these command :
rbcavity -r rdock.prm -d -was > cavity.log
rbdock -r rdock.prm -p dock.prm -n 200 -i lig_org.sdf -o docking_out > docking_out.log
( I get stuck here)
sdsort -n -s -fSCORE docking_out1.sd | sdfilter -f'$_COUNT == 10' > docking_out_sdfilter1.sd
sdreport -t docking_out_sdfilter.sd | awk '{print $2,$3,$4,$5,$6,$7}' > dataforR_uq.txt
I also attached some files. I am running on computecanada clusters.
Best,
Sam