corrected some docs

doc/doc_mol22lt.md

@@ -58,41 +58,11 @@ and combined with (bonded to) other molecules, as demonstrated in the
 
 
 ## *WARNING: THIS SOFTWARE DOES NOT WORK WITH MULTIPLE CHAINS*
-This software does not work with MOL2 files
-containing multiple "chains".
+This software does not work with MOL2 files containing multiple "chains".
 *("Chains" are optional features located in the
 [SUBSTRUCTURE section of some MOL2 files](http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf).)*
-As a workaround, if your MOL2 file contains multiple chains,
-split it into multiple MOL2 files (one per chain).
-Then convert each file separately.
-Afterwards, if you want to define a large molecular complex
-(such as a protein with quaternary structure),
-you can use moltemplate to define a large molecule composed of
-multiple chain subunits.  For example, suppose we have a .mol2 file containing
-two chains. If we split that file into two files ("chainA.mol2", "chainB.mol2"),
-we can create two .lt files, one for each chain:
-```
-mol22lt.py --in chainA.mol2 --out chainA.lt --name ChainA --ff GAFF2 --ff-file "gaff2.lt
-mol22lt.py --in chainB.mol2 --out chainB.lt --name ChainB --ff GAFF2 --ff-file "gaff2.lt
-```
-Then we can then can manually create a new .lt file
-(eg. "protein_with_2_chains.lt")
-defining a molecular complex containing two chains:
-```
-import "chainA.lt"  # Defines "ChainA"
-import "chainB.lt"  # Defines "ChainB"
-ProteinWith2Chains {
-  a = ChainA
-  b = ChainB
-}
-```
-And then (in our "system.lt" file) we can instantiate that
-complex this way (for example):
-```
-protein1 = new ProteinWith2Chains
-```
-(-Andrew 2024-12-06)
-
+However there is a manual workaround.
+([See below](#working-with-multiple-chains).)
 
 
 ## Details
@@ -299,6 +269,39 @@ Make sure they remain uniquely named, even after changing capitalization.)*
 
 
 
+## Working with multiple chains
+
+As a workaround, if your MOL2 file contains multiple chains,
+split it into multiple MOL2 files (one per chain).
+Then convert each file separately.
+Afterwards, if you want to define a large molecular complex
+(such as a protein with quaternary structure),
+you can use moltemplate to define a large molecule composed of
+multiple chain subunits.  For example, suppose we have a .mol2 file containing
+two chains. If we split that file into two files ("chainA.mol2", "chainB.mol2"),
+we can create two .lt files, one for each chain:
+```
+mol22lt.py --in chainA.mol2 --out chainA.lt --name ChainA --ff GAFF2 --ff-file "gaff2.lt
+mol22lt.py --in chainB.mol2 --out chainB.lt --name ChainB --ff GAFF2 --ff-file "gaff2.lt
+```
+Then we can then can manually create a new .lt file
+(eg. "protein_with_2_chains.lt")
+defining a molecular complex containing two chains:
+```
+import "chainA.lt"  # Defines "ChainA"
+import "chainB.lt"  # Defines "ChainB"
+ProteinWith2Chains {
+  a = ChainA
+  b = ChainB
+}
+```
+And then (in our "system.lt" file) we can instantiate that
+complex this way (for example):
+```
+protein1 = new ProteinWith2Chains
+```
+
+
 ## Python API
 
 It is possible to access the functionality of *mol22lt.py* from