molecules. Remove all but one population of them. Similarly,
look for residues which exist in alternate conformations (ALYS,
BLYS, etc.). Select one of them for further processing, remov-
ing the rest. Also, correct partially built residues, such as surface
side-chains with atoms missing as a result of local disorder.- Decide on the protonation state of residues such as HIS and
CYS (in some cases ASP and GLU side chains may also be
protonated). HIS becomes HID, HIE or HIP, if protonated
in position delta, epsilon or both, respectively. Deprotonated
cysteines and those bound to metal atoms become CYM, while
those involved in disulphide bridges become CYX (seeNote 3). - To create a disulphide bridge, use a tleap command such as
“bond mol.X.SG mol.Y.SG”, where mol is the object holding
the protein structure, while X and Y stand for the residue
numbers of cysteines involved. The residue numbers typically
start from the first number in the PDB file and continue
sequentially through chains and all extras, such as ions
and ligands. Type "desc mol" in tleap to see all residue num-
berings. We use tleap rather than xleap to be independent of
the graphical platform used, and to be able to include this
command in batch scripts. We launch tleap on a predefined
set of scripts (e.g., “tleap –f script.txt”). An example of a tleap
script follows:
source leaprc.ff03 #(make sure that this is in the path of the program)
set default PBradii mbondi2 #(for affinity calculations;seeSubheading 3.7)
mol=loadpdb prot.pdb #(loads the cleaned and completed PDB file)
list #(checks the contents)
check mol #(there should be no missing parameters)
bond mol.10.SG mol.20.SG #(example of a bridge between Cys10 and Cys20)
saveamberparm mol rec.prmtop rec.inpcrd #(create topology files)
savepdb mol rec.pdb #(optionally save the new PDB file)
quit
In the above the saveamberparm command allows keeping
the topology of the receptor, which will be needed at the
analysis stage. The script checks if the structure and topology
are correct (seeNote 4). Should this not be the case, error
messages will appear, helping to identify the source of the
problem, which should be corrected before continuing.- If there are ions present in the structure (Mg2+,Zn2+,...), treat
each as a separate residue (i.e., insert TER before and after each
line on which an ion is placed). Change the atom and residue
names to those recognized by the force field used, such as ff03
in the example above (e.g., for chlorine: use "Cl–" in the fields
of both atom and residue names).
Molecular Dynamics in Virtual Screening 151