README.md

Host for the SAMPL7 TrimerTrip Challenge

The Trimertrip host structure was originally provided by Lyle Isaacs as a CIF file from crystallography. However, to avoid biasing results we are not releasing this structure at present, and instead equilibrated a structure of the host (details of this setup can be found below) which we are providing here in SDF, MOL2 and PDB formats. The original structure from crystallography will be provided here once the challenge concludes.

• The Trimertrip host files were created as follows:
  • Original starting structure (in CIF file format, which will be added here once the challenge ends) was converted to a PDB using OpenEye toolkits. Water, a guest, a single Na+ ion, and connectivity records were manually removed. OpenEye toolkit was used add explicit hydrogen and saved to a PDB. The PDB was manually inspected and missing protons were manually added, and the corrected structure was saved to a PDB. OpenEye toolkit was used to normalize the molecule, assign partial charges using AM1-BCC and save the resulting molecule to a MOL2 file. The SYBYL atom types in the MOL2 file were switched to GAFF2 atom types using antechamber, as the parmchk2 toolkit used afterwards expects GAFF/GAFF2 atom types. The parmchk2 toolkit was used to generate parameters and a frcmod file and these files were used in tleap (adding TIP3P water and sodium chloride) to generate amber files. The OpenMM toolkit was used to briefly run some dynamics to generate an amber compatible NetCDF coordinate file with initial velocities. Afterwards, an annealing procedure was used where the structure was heated from 0K to 450K for 30ps, then kept at kept at the high temperature for 5ns, then cooled to room temperature (273K) for 30ps and then kept at this temperature for 10ns. The RMSD of the final Trimertrip structure from the starting crystal structure is 3 Angstroms.
  • File creation: The pytraj toolkit (the python interface of cpptraj, which is a part of AmberTools) was used to remove the solvent (water, Na+ and Cl-) and create a MOL2 file, then the antechamber toolkit was used to convert GAFF2 atom types to SYBYL/Tripos atom type, the resulting MOL2 file was read into OpenEye and written out to a new standards-compliant MOL2 file, this MOL2 file was then used to generate a SDF and PDB file using OpenEye tools.

What's here

• SAMPL7.cdx Chemdraw of the guests and TrimerTrip host provided by Isaacs. Note, the jpg file in the images folder one directory above was generated by Mobley from this Chemdraw file. This Chemdraw file is the same as the one found in the guest_files folder one directory above.