Use case: thrombin

[jmichel80]

=== Attachment ===
Input: 2zc9.pdb
Output: thrombin-allatom-ready.pdb

=== Setup description ===
The crystallographic structure of human thrombin in a complex with a
thrombin ligand structurally related to the ligands simulated in this
study was downloaded from the PDB databank (PDB code 2ZC9). The
protein structure was inspected and prepared for molecular simulations
using Maestro. The hirugen chain was removed from the structure. The
side chain of Arg75 in the heavy chain (chain H) of thrombin was
partially resolved. Missing atoms were added to complete the side
chain in a solvent-exposed conformation. The incomplete light chain
was capped before Glu1C with an ACE residue and after Ile14L with an
NME residue.19 The incomplete heavy chain was capped after Gly246 with
an NME residue.19 Missing residues Trp148, Thr149, Ala149A, Asn149B,
Val149C, Gly149D, and Lys149E in chain H were modeled in the structure
using the FALC-Loop Webserver. Standard protonation states were
assumed for protein side chains. On the basis of visual inspection
of hydrogen bonding patterns, His57 and His71 were modeled in their
uncharged δ-tautomer. His91, His119, and His230 were modeled in the
δ-tautomer. Disulfide bridges were modeled between Cys42−Cy

thrombin.zip