Desmond Tutorial

Desmond Tutorial
Finishing Preparations for Desmond Simulation
field provides the dihedral parameters for the same residues. The force field components
should be disjoint so there is no conflict with the parameters that are assigned to each
component.
You may also use multiple force fields when parameters assigned to a particular residue
by one force field override parameters assigned by another force field. This situation is
similar to combining force fields; residues in the chemical system match templates in
more than one of the specified force fields and all matching force fields are applied.
However, in this case two or more force fields provide parameters for the same term; for
example, two force fields provide parameters for the angle between atoms 1, 2, and 3
causing a conflict. The conflict is resolved by allowing the first force field (that matches
the residue) to take precedence. The order is the order in which the force fields were
specified on the command line.
In all multiple force field assignment cases, Viparr prints an error message and aborts if a
bond exists between two residues that are not matched by the same force field.
The selected force fields should also have consistent van der Waals combining rules.
Otherwise, Viparr will abort with an error message.
Viparr will print the following warning and error messages when matching residues to
templates:
• If any residue matches more than one template in a force field, then Viparr exits with
an error. (No Viparr force field should contain identical templates.)
• If any residue name is matched to a force field template with a different name, a
message is printed. A maximum of 5 messages are printed per residue‐template
name pair.
• Viparr will check that all residues are matched by one of the selected force fields. If
there are any unmatched residues, Viparr will print all unmatched residues and exit
with an error. A maximum of 5 messages are printed per unmatched residue name.
• If any residue is matched by more than one of the selected force fields, Viparr will
print a warning message. The user should be cautious and be responsible for any
intended use of multiple force fields with multiple matches.
Besides the -f option, there are two more basic options. The -c option allows the user to
assign parameters for a particular structure (CT block) in the input .cms file and the -n
option provides a means to include a user‐defined comment in the output .cms file for
annotation purposes.
Viparr also supports user‐defined, special force fields (the -d, -m, and -p options), but
that is beyond the scope of this tutorial. Please refer to the Desmond User Guide for information.
Specifying Desmond Simulation Parameters
Before it can perform simulations, Desmond needs certain simulation parameters to be
set. These parameters can be set in two ways:
• Using the Run Desmond facility in Maestro.
• Editing the Desmond conguration file directly.
The following sections provide more details on each option.
60 D. E. Shaw Research September 2008