Hands-on items

_episodes/14-Preparing_Protein-Membrane_System.md

@@ -124,55 +124,6 @@ quit
 `--salt`
 
 
-## Generating topologies and parameters for small molecules.
-
-### Automate Topology Builder web service. 
-[ATB](https://atb.uq.edu.au) is limited to GROMOS 54A7 force field.
-
-
-### ANTECHAMBER
-- Download hexanediol HEZ.cif: wget https://www.rcsb.org/ligand/HEZ
-- Convert .cif to .pdb: https://mmcif.pdbj.org/converter/index.php?l=en
-
-1. Make mol2 file with antechamber:
-
-~~~
- module load StdEnv/2020 gcc cuda/11.4 ambertools/22
- antechamber -i HEZ.pdb -fi pdb -o HEZ.mol2 -fo mol2 -c bcc -s 2
-~~~
-{: .language-bash}
-
-The file HEZ.mol2 contains the definition of our HEZ residue including connectivity, all of the charges and atom types. 
-
-2. Run parmchk2 to find out if there are any missing force field parameters:
-
-~~~
- parmchk2 -i HEZ.mol2 -f mol2 -o HEZ.frcmod
-~~~
-{: .language-bash}
-
-If it can antechamber will fill in these missing parameters by analogy to a similar parameter.
-
-3. Create the library file for HEZ using tleap:
-
-~~~
-source leaprc.gaff2
-HEZ=loadmol2 HEZ.mol2
-check HEZ
-saveoff HEZ hez.lib 
-~~~
-{: .leap}
-
-Of course point charges are not very accurate because they are derived using semi-empirical method, but antechamber can also use results of gaussian QM calculations.  
-
-### AnteChamber PYthon Parser interfacE (ACPYPE)
-
-[ACPYPE - AnteChamber PYthon Parser interfacE](https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-5-367). 
-
-- Simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programs.
-
-
-
 ### Links to advanced AMBER tutorials
 - [Placing waters and ions using 3D-RISM and MOFT](http://ambermd.org/tutorials/advanced/tutorial34/index.html)
 - [Building a Membrane System with PACKMOL-Memgen](https://ambermd.org/tutorials/advanced/tutorial38/index.php#Lipid_System)