Hello everybody:
I´m trying to performance a blind docking in Swissdock but when I upload de ligand in .mol2 saved whit Chimera, this show me a problem, and told me that check its topology I take the ligands from a previous docking pdb using comands in Linux
I will be glad if somebody can help me
Daniel
Thanks Peter:
But I already read that in the docking page of Swissdock, and how I say Im using UCSF Chimera to prepare the .mol2 file, and even so the problem that I mentioned above persist. Do you know if the problem could be in the way that I take the ligands?
Hi Peter:
The previous .pdb files that I use, I downloaded this from Protein Data Bank so I assume that they were ok If you want I cant upload one file so you can see the topology
Peter, I already resolved the problem using the PRODRG server to generate the .MOL2 and the Swissdock accepted the file Thanks for your time and your answers
Hi Daniel,
I am facing same problem, i.e., when I am trying to upload ligand (mol2 file generated using chimera of a structure downloaded from PDB) in swissdock, the error messege saying that the topology is incorrect is shown.
Could you please elaborate bit more about resolving them?
Hi Deepti:
I solved that problem using the web server PRODROG, it`s a server that generate several files using the coordinates from your original file Try using it
I hope that this can be useful for you
Hi Daniel,
Thank you! I will try this.
I have also tried GRAMM-X, it's satisfactory.
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