Dear all,
I just downloaded the tranches from zinc 20 database. but the files are in gz format. this means each on of them has to be extracted.
is that correct
if yes then extracting data from each one is going to be the most time consuming work.
anyone has experience otherwise?
Thank you
Ayesha
Hi all.
I managed to solve part of this problem, i.e., extracting the files by creating a bash script.
Now the next issue is that each file that is extracted has more molecules per file that can be split using obabel.
I made a script that runs within the folder with the pdbqt merged file. However, I cannot run the script from. Outside the folder. It goes inside the folder but gives the error that it cannot read the pdbqt.
Since there are several folders downloaded from. Zinc, it is imperative to run the script.
Anyone has ideas, will appreciate very much.
Thank you
Hi Ayesha Fatima could you please guide me how do i extract the files from the .sdf.gz file, as i have used powershell to extract them and i am having issues from few tranches, or could you guide me if there is any other way
The error (it occurs 4 time maybe for 4 different tranches):
Invoke-WebRequest : Forbidden You don't have permission to access this resource. At C:\Users\mohds\Desktop\New folder\ligand_pdbqt.ps1:19 char:41 + ... directory; Invoke-WebRequest http://files.docking.org/3D/FD/CBRN/FDC ... + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CategoryInfo : InvalidOperation: (System.Net.HttpWebRequest:HttpWebRequest) [Invoke-WebRequest], WebExc eption + FullyQualifiedErrorId : WebCmdletWebResponseException,Microsoft.PowerShell.Commands.InvokeWebRequestCommand
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