Epik output

[SalahBioPhysics]

In Erlotinib, the Erlotinib-epik-charged.mol2 doesn't match with Erlotinib-epik.mol2. The later has two tautomers, but Erlotinib-epik-charged.mol2 has only one, its also missing the H53 charge.

[SalahBioPhysics]

In Vemurafenib, the Vemurafenib-epik-charged.mol2 doesn't match with Vemurafenib-epik.mol2. The later has four tautomers, but Vemurafenib-epik-charged.mol2 has two tautomers.

[SalahBioPhysics]

In Palbociclib, the Palbociclib-epik-charged.mol2 doesn't match with Palbociclib-epik.mol2. The later has four tautomers, but Palbociclib-epik-charged.mol2 has two tautomers.

[SalahBioPhysics]

In Ruxolitinib, the Ruxolitinib-epik-charged.mol2 doesn't match with Ruxolitinib-epik.mol2. The later has two tautomers, but Ruxolitinib-epik-charged.mol2 has one tautomers.

[jchodera]

Thanks for pointing these out!

The reason for this is that some of the protomers/tautomers fail at the charging step. Often, this is because the proposed protomers/tautomers are so unphysical that the Omega/AM1-BCC charging scheme can't deal with them, and it is fine that this happens. In other cases, this is a serious issue that we have to find some way to address.

The next step would be to figure out if the dropped tautomers/protomers are reasonable. If so, we can take these to Christopher Bayly and have them fix the charging scheme.

For now, the best thing to do is to always rely on the -epik-charged.mol2 files, since these have already been filtered for "reasonableness" by the charging scheme.

[SalahBioPhysics]

Ok sounds good. We will go with -epik-charged.mol2.

Thanks :)