"platforms/cpu/src/CpuCustomGBForce.cpp" did not exist on "0843c5f34651bf49f418f5336a9b7bafc2b8f89a"
Unverified Commit 551d83c9 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Minor clarification to manual (#3362)

* Minor clarification to manual

* Another minor clarification
parent 0c82c264
......@@ -78,6 +78,7 @@ The :code:`<ForceField>` tag contains the following children:
* An :code:`<AtomTypes>` tag containing the atom type 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
......@@ -203,18 +204,20 @@ Here is an example of a patch definition:
.. code-block:: xml
<Patch name="NTER">
<RemoveAtom name="H"/>
<RemoveBond atomName1="N" atomName2="H"/>
<AddAtom name="H1" type="H"/>
<AddAtom name="H2" type="H"/>
<AddAtom name="H3" type="H"/>
<AddBond atomName1="N" atomName2="H1"/>
<AddBond atomName1="N" atomName2="H2"/>
<AddBond atomName1="N" atomName2="H3"/>
<RemoveExternalBond atomName="N"/>
<ChangeAtom name="N" type="N3"/>
</Patch>
<Patches>
<Patch name="NTER">
<RemoveAtom name="H"/>
<RemoveBond atomName1="N" atomName2="H"/>
<AddAtom name="H1" type="H"/>
<AddAtom name="H2" type="H"/>
<AddAtom name="H3" type="H"/>
<AddBond atomName1="N" atomName2="H1"/>
<AddBond atomName1="N" atomName2="H2"/>
<AddBond atomName1="N" atomName2="H3"/>
<RemoveExternalBond atomName="N"/>
<ChangeAtom name="N" type="N3"/>
</Patch>
</Patches>
There is one :code:`<Patch>` tag for each patch definition. That in turn may
contain any of the following tags:
......
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