Skip to content

GitLab

Unverified Commit 551d83c9 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
Browse files

Minor clarification to manual (#3362) 

* Minor clarification to manual

* Another minor clarification
parent 0c82c264
Hide whitespace changes
Inline Side-by-side
Showing with 15 additions and 12 deletions
docs-source/usersguide/application/05_creating_ffs.rst
View file @ 551d83c9
...@@ -78,6 +78,7 @@ The :code:`<ForceField>` tag contains the following children: ...@@ -78,6 +78,7 @@ The :code:`<ForceField>` tag contains the following children:
* An :code:`<AtomTypes>` tag containing the atom type definitions * An :code:`<AtomTypes>` tag containing the atom type definitions
* A :code:`<Residues>` tag containing the residue template definitions * A :code:`<Residues>` tag containing the residue template definitions
* Optionally a :code:`<Patches>` tag containing patch definitions
* Zero or more tags defining specific forces * Zero or more tags defining specific forces
...@@ -203,18 +204,20 @@ Here is an example of a patch definition: ...@@ -203,18 +204,20 @@ Here is an example of a patch definition:
.. code-block:: xml .. code-block:: xml
<Patch name="NTER"> <Patches>
<RemoveAtom name="H"/> <Patch name="NTER">
<RemoveBond atomName1="N" atomName2="H"/> <RemoveAtom name="H"/>
<AddAtom name="H1" type="H"/> <RemoveBond atomName1="N" atomName2="H"/>
<AddAtom name="H2" type="H"/> <AddAtom name="H1" type="H"/>
<AddAtom name="H3" type="H"/> <AddAtom name="H2" type="H"/>
<AddBond atomName1="N" atomName2="H1"/> <AddAtom name="H3" type="H"/>
<AddBond atomName1="N" atomName2="H2"/> <AddBond atomName1="N" atomName2="H1"/>
<AddBond atomName1="N" atomName2="H3"/> <AddBond atomName1="N" atomName2="H2"/>
<RemoveExternalBond atomName="N"/> <AddBond atomName1="N" atomName2="H3"/>
<ChangeAtom name="N" type="N3"/> <RemoveExternalBond atomName="N"/>
</Patch> <ChangeAtom name="N" type="N3"/>
</Patch>
</Patches>
There is one :code:`<Patch>` tag for each patch definition. That in turn may There is one :code:`<Patch>` tag for each patch definition. That in turn may
contain any of the following tags: contain any of the following tags:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment