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 Post subject: Ligand file format
PostPosted: Tue Dec 08, 2009 11:58 pm 

Joined: Tue Dec 08, 2009 11:01 pm
Posts: 5
I have problem with uploading my ligand file. I found my lignad compound in Pubchem. However, there are only 3 available file formats for downloading, ASN, XML and SDF. Among these, only SDF is allowed in Dockingserver, but it is applicable under free subscription. Right now, I'm just running this for a testing and not ready for advanced services yet. I could not find out how to convert SDF to PDB or other applicable files yet. What should I do?

PittSB


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 Post subject: Re: Ligand file format
PostPosted: Wed Dec 09, 2009 4:33 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
You have more options. First, PubChem is integrated into DockingServer, thus using the "Download from Pubchem" button you can download the ligand directly into your DockingServer account; this is the easiest way in my opinion. Second option is to download the Sdf file from Pubchem and rename its extension to "mol" and upload it to DockingServer. This will work, because only multiple-ligand sdf files are disabled for free users and Pubchem sdf files are mol files in reality.

Zsolt


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 Post subject: Re: Ligand file format
PostPosted: Wed Dec 09, 2009 8:35 pm 

Joined: Tue Dec 08, 2009 11:01 pm
Posts: 5
It works well now. Thank you very much!


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