Maestro User Manual

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

108

4. When the desired point group is found, click 

Symmetrize

. 

Structures that are built by drawing, or have been adjusted manually, can be far from the

minimum energy structure. To “clean up” the structure in the Workspace, the Geometry

Cleanup utility minimizes the energy of the structure or of the selected atoms using either the

built-in minimizer with the OPLS_2005 force field, or the Universal Force Field (UFF). The

choice of minimizer and force field can be set either from the 

Clean Up

 button menu or in the

Preferences

 panel (see 

Section 14.12 on page 371

). 

Cleanup realigns atoms that are too crowded and corrects unphysical geometries. In general, it

corrects distortions that can cause jobs to fail, such as MacroModel or Jaguar jobs. Minimiza-

tion proceeds for 300 cycles or until the maximum atom displacement is less than 0.05 Å. By

default, when using the built-in minimizer, atoms within 5 Å of the selected atoms are

restrained with a moderate restraint, and atoms within 5 Å of these atoms are restrained with a

much tighter restraint. The rest of the atoms are frozen, but you can set a preference to freeze

all unselected atoms—see 

Section 14.12 on page 371

.

To run this utility, choose 

Edit 

→

 Build 

→

 Clean Up Geometry

, press 

U

, or click the 

Clean Up

button on the 

Build

 toolbar. This job is not run at reduced priority, unlike most local jobs.

You can also use the built-in minimizer on the selected atoms by choosing 

Tools 

→

 Minimize

→

 Selected Atoms 

or pressing 

CTRL+M

  (

M

), which minimizes for 1000 cycles or a

maximum displacement of 0.01 Å. If no atoms are selected, all atoms are minimized. To mini-

mize the ligand, choose 

Tools 

→

 Minimize 

→

 Ligand 

or press 

CTRL+SHIFT+M

 (

M

).

5.10 Adding and Treating Hydrogen Atoms

When building molecules or preparing proteins, you might want to apply a hydrogen treatment

that is compatible with the force field you intend to use in calculations on those structures. You

can also use a hydrogen treatment to add hydrogen atoms to a structure that is used for any

program that requires explicit hydrogen atoms, such as QikProp or Jaguar. Hydrogen treat-

ments can treat hydrogen atoms explicitly or implicitly, as part of another atom. To select and

apply a hydrogen treatment, you can use the controls in the 

Add Hydrogens - Advanced

 panel,

which you open by choosing 

Edit 

→

 Add Hydrogens 

→

 Advanced

.

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Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

109

Figure 5.11. The Add Hydrogens - Advanced panel.

To select a hydrogen treatment, choose an option from the 

Treatment 

option menu. A descrip-

tion of the treatment is displayed in the 

Description

 text box, including the force fields for

which the treatment is valid. This information is also given in 

Table 5.2

. 

You can apply the selected treatment to the entire structure or to selected parts of the structure.

To apply the treatment to the entire structure click 

All 

in the 

Modify Hydrogen Treatment

section. To apply the treatment to selected atoms, use the picking tools in the 

Modify Hydrogen

Treatment

 section or click 

Select

 to open the 

Atom Selection

 dialog box and define the selected

atoms. If the structure already complies with the treatment you selected, no changes will be

made when you apply the treatment.

You can also apply the current hydrogen treatment to selected atoms, molecules, residues,

chains, or entries from the main toolbar or the 

Build

 panel toolbar. Select one of these structural

units from the 

Add H

 button menu, 

then pick atoms in the Workspace to apply the treatment. Double-click this button to apply the

treatment to all atoms in the Workspace. 

Each time you select a force field in the 

Potential

 section of a MacroModel or Impact energy

panel, the hydrogen treatment is automatically changed to comply with that force field, and the

hydrogen treatment for any atoms you subsequently draw in the Workspace will have the new

hydrogen treatment. If you attempt to start a MacroModel, Impact, or Jaguar job using an input

structure with an incompatible hydrogen treatment, the job fails.

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Chapter 5: Building and Adjusting Structures

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5.11 Changing Atom Properties

In addition to changing the element and the formal charge, you can change a variety of other

atom properties. The tools for making changes are in the 

Atom Properties 

tab. Each choice of

property from the 

Property

 option menu displays a set of tools that you can use to change the

property. Apart from the 

Element

 property, the properties are listed below with a description of

the tools. The last item on the option menu, 

Other

, allows you to change the values for any

other atom property.

Before you change atom properties, it may be helpful to display atom labels. For atom labeling

information, see 

Section 8.2 on page 162

.

5.11.1

Atom type (MacroModel) 

When you choose 

Atom type (MacroModel)

 from the 

Property

 option menu, a list of atom type

symbols with a brief description is displayed (see 

Figure 5.12

). The atom type symbols repre-

sent atoms with specific properties, such as sp

3

 hybridization for a C atom with type symbol

C3, or a free radical for a C atom with type symbol CR. To retype an atom, choose the atom

type and click on the atoms in the Workspace that you want to change.

The use of atom types is provided primarily for MacroModel users, though Maestro always

assigns an atom type to each atom. For information on atom types, see 

Appendix B

.

Table 5.2. Appropriate hydrogen treatments for Maestro-supported force fields.

Hydrogen Treatment 

Method

MM

3

MM

2

AMBER

AMBER94

MM

FF

MM

FFS

OPLS-AA,

OPLS_20

0x

OPL

S

All-atom  with  No-Lp

X

X

X

X

X

X

All-atom with Osp3-Lp

X

Csp3 United-atom with 

S-Lp

a

X

Csp3 United-atom with 

No-Lp

a

X

All atom with S-Lp

X

Csp2/sp3 United atom 

with No-Lp

a

X

a. In a united atom representation, hydrogen atoms are incorporated into the dimensions of the heavy 

atom to which they are attached. That is, they are implicit.

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