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GLYCAM-Web / MD_Utils

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Save better solvated PDB files #3

Closed Lachele closed 9 months ago

Lachele commented 2 years ago

The solvated PDB files contain no CONECT cards. They also have TER cards between each residue. They are currently being written by tleap. See if some other utility in AMBER will do a better job generating the files.

Lachele commented 9 months ago

Update: we have cpptraj write the files out now. There are ter cards, but no conect cards. That is an improvement.

gitoliver commented 9 months ago

We only produce these solvated files: unminimized-t5p.parm7 unminimized-t5p.pdb unminimized-t5p.rst7. The pdb file has TER cards between each residue, but no bonding information. If you load this into tleap you'll have to manually add bond commands. For linear oligos you can just remove the TER cards. For branched ones you'll have to either add bond commands for everything, or keep TER cards at branches and add bonds just for those. Ideally we have TER cards between each residue and CONECT cards specifying what to bond.

gitoliver commented 9 months ago

Er actually, if you want to simulate these just use unminimized-t5p.parm7 and unminimized-t5p.rst7. If you want to load a solvated system into tleap (unminimized-t5p.pdb), well better to just load the unsolvated min-gas.mol2 file. It has charges and connectivity. Look in unminimized-t3p.leapin or unminimized-t5p.leapin for how we generate the unminimized-t5p.* files from min-gas.mol2. Suggest close?

Lachele commented 9 months ago

Yes. I'm good with closing this one.