Is there any tutorial for how to manually write the topology file for any Ligand file(PDB for mol2)? There are so many sites which provides it like ProDrug or ATB but no where the actual process is written. Can anyone explain the process?

PS: I am actually not sure this question belong to which SO.


First off, you should not be manually writing topology files whenever you can avoid it - it's far too prone to making silly errors. That's why there are so many programs out there that attempt to automate the process.

If however, you just want to understand HOW the topology file is structured, I recommend reading the GROMACS manual (chapter 5). These tutorials also do a good job of describing some of the key aspects of the topology files.

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  • $\begingroup$ Thanks for the answer but I know the tutorial and I have mentioned both ProDrug and ATB. But every time get errors so here in this post they ask to write it manually. Can you suggest any offline tool? $\endgroup$ – Devashish Das Aug 7 '14 at 15:06
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    $\begingroup$ From the tutorials I linked, here are a few tools used for different forcefields. Not all of them are actively maintained so you do need to actually understand how the topology SHOULD look and double check the output. You should really take some time to read the chapter in the manual so you understand the structure of the files. bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/… $\endgroup$ – CTKlein Aug 7 '14 at 15:09

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