Differences between `pdb2pqr` as standalone and via htmd

[aanastasiou]

There seem to be some differences between the standalone version of pdb2pqr and the one provided by htmd and I was wondering what these differences are due to (?).

As we can see here, there are 3 versions with slight differences:

1. The standalone pdb2pqr does not have any "extensions" and also, does not list --ph-calc-method as a parameter
2. The htmd version includes a number of "extensions" to output hydrogen bonds, contacts, salt bridges etc.
3. The standalone version provides a pdb2pqr30 while the htmd one provides a pdb2pqr_cli

Is it possible to clarify what these differences are due to please? On the htmd provided pdb2pqr, extensions is a package, but it is not there on the standlone pdb2pqr. Is that a separate dependency?

I am interested in those extensions which seem to be listed on precompiled versions (e.g. the one that is available on Debian) but not there across all uses of pdb2pqr.

[stefdoerr]

Γειά σου Θανάση :) Tricky question because I've not kept up with it. I would suggest you use the official version since they have updated it recently to 3.0. Ours is a fork from 2.1.1 version with some fixes. Specifically I remember fixing one issue where the added atoms were just copying the element of the first atom of the residue it was being added to, so the hydrogens would end up having carbon element which caused some issues in our pipeline. But they might have fixed this since then in the official version. I'm not sure what the extensions package is for, sorry

[aanastasiou]

Γειά σου Στέφανε! :)

The 3.0.0 seems to have renamed some options (which is fine) but the options on listing hydrogen bonds, contacts and salt bridges are not there. The 2.1.1 has those options but it also includes extensions which is not there in 3.0.0. But I might ask over at pdb2pqr.

Thank you anyway, it was an opportunity for me to get to know about htmd too :)

All the best