The target is known, the ligands which I have taken,I am getting error,which other free softwares can be used?
Initially try building a pharmacophore model with the given examples in Pharmagist.. and look at the FAQ: http://bioinfo3d.cs.tau.ac.il/pharma/faq.html. Once you are experienced then model with your set of ligands. if your still facing difficulties post your error message s here.
I am getting the error as An error occured in your pharma run. Please check your molecule file. I have used pharmagist before and this is the first time I am getting the message.
If you want to perform a "Docking" simulation, I think that you could try using Autodock 4. It is free.
Well i have docked the individual ligands with my protein via Autodock vina.
Hello Prajakti ,
I am a continuous user of PharmaGist , hence i think i can help you. before running next time please consider these.
1.) dock your candidates and obtain their Bio-Active Conformations of all the ligands.
2.) Make sure that all hydrogens are added in your molecule file.
3.) Make sure your molecule is in .MOL2( SYBL Mol2 file), and not just in .MOL file.. Use OpenBabel to sort out this.
4.) try to avoid the Sterochemistry bonds , sometimes it throws error message because of the Sterochemistry projection bonds..
Well like this i can still state some checks , but for now i thing your problem will be sorted within the above mentioned checks , If not , we'll discuss further.
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ok yes I can try it out! I really did dock the molecules individually.
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