1. antechamber: strange molecules get parameter files
Amber 10 Tutorial
antechamber: strange molecules get parameter files

2. antechamber & leap
antechamber is predominantly a file converter. However, it can be used in conjunction with leap to build parameter files that can be used to run MD and other simulations.

3. sustiva.pdb
ATOM C1 SUS
ATOM H1 SUS
ATOM C2 SUS
ATOM C3 SUS
ATOM C4 SUS
ATOM C5 SUS
ATOM C6 SUS
ATOM H2 SUS
ATOM C7 SUS
ATOM H3 SUS
ATOM H4 SUS
ATOM C8 SUS
ATOM H5 SUS
ATOM H6 SUS
ATOM C9 SUS
ATOM F1 SUS
ATOM F2 SUS
ATOM F3 SUS
ATOM O1 SUS
ATOM C10 SUS
ATOM O2 SUS
ATOM N1 SUS
ATOM H7 SUS
ATOM C11 SUS
ATOM C12 SUS
ATOM H8 SUS
ATOM C13 SUS
ATOM H9 SUS
ATOM C14 SUS
ATOM Cl1 SUS
What makes the antechamber/leap combination so powerful is the original format of the information that is fed into it.
Notice that on the left there is no detailed information given. Only atom #, atom type, and position. With this antechamber and leap can generate parameter files.
The SUS label on the atoms here is important because it will be the label leap will use later for the sustiva unit.

4. antechamber
to generate the amber PREP files for sustiva (later used by leap to generate the parameter files) we run antechamber.
>> antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2
-i: means input file
-fi: means input file format (which is pdb in this case)
-o: the name we wish the output file to have
-fo: the format we wish the output file to have
-c: the charge method we wish to use to build charges for out SUS system
bcc: BCC (AM1-BCC) used to calculate charges of the atoms
-s: this sets the verbosity of the output from antechamber
These output options can be seen in the “Amber10Tools.pdb” on pg 66 & 67.

5. antechamber outputs
Note: antechamber will create a lot intermediate files. These files will all be CAPITALIZED and can be deleted. They are only useful if something went wrong in antechamber.
Also some divcon files will be generated. They are used to show how the charges of the atoms were found via quantum mechanics.
4 AchamberSUS.sh* ATOMTYPE.INF 4 sus.leap
4 ANTECHAMBER_AC.AC delete.com* sustiva.crd
4 ANTECHAMBER_AC.AC divcon.pdb sustiva.frcmod
4 ANTECHAMBER_AM1BCC.AC leap.log sustiva.pdb
4 ANTECHAMBER_AM1BCC_PRE.AC 4 mopac.in sustiva.prepin
4 ANTECHAMBER_BOND_TYPE.AC mopac.out sustiva.top
4 ANTECHAMBER_BOND_TYPE.AC mopac.pdb sustivawh2o.lpdb
4 ANTECHAMBER_PREP.AC NEWPDB.PDB
4 ANTECHAMBER_PREP.AC PREP.INF

6. parmchk
parmchk is used to check the parameters in our newly generated sustiva.prepin file.
>> parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod
-i: means input file
-f: means input file format (which is prepi in this case)
-o: the name we wish the output file to have
*.frcmod is a force-field modification file. This will contain missing or all forcefields that are needed for you system.
These output options can be seen in the “Amber10Tools.pdb” on pg 68.

7. Now to LEAP
I will assume you have read the leap tutorial or have basic understanding of leap here.
Normally we load one set of force-field parameters into leap. However with antechamber we load our generic ff03 and also gaff
source leaprc.ff03
source leaprc.gaff
gaff is a force-field set used for antechamber and can be used in conjunction with other force-fields.

8. in LEAP
Then we load our sustiva information into leap from out sustiva.prepin file generated earlier:
loadamberprep sustiva.prepin pg 45 tools
loadamberprep loads in an amber prepin file. The key here is that a new unit is created for every “residue” in the prepin file. i.e. You would have more units if you had more than 1 type of label for objects in your original pdb file.
If you type “list” in leap now you will see a unit titled SUS listed. This unit is labeled SUS because it was labeled this in the original pdb file (sustiva.pdb)

9. in LEAP now check if everything is o.k. with our SUS unit.
check SUS
Checking 'SUS'....
Checking parameters for unit 'SUS'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: ca - c3 - c1
Could not find angle parameter: c1 - c1 - cx
Could not find angle parameter: c1 - cx - hc
Could not find angle parameter: c1 - cx - cx
There are missing parameters.
Unit is OK.
I believe the program is lying to you here, unit is NOT o.k. :P.
Could not find angle parameter: … is a bad thing.

10. in LEAP
To fix your angle parameter problem we load in our modified force field file that parmchk has given us (sustiva.frcmod).
loadamberparams sustiva.frcmod pg 45 tools
this will load the parameters contained within the file sustiva.frcmod into the general amber parameters. these will be used if needed by any unit.
Now recheck the SUS unit
check SUS
Checking 'SUS'....
Checking parameters for unit 'SUS'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Now our SUS unit is O.K!

11. Output parameter files and pdb
Now we just output our new parameter file and save a copy of our pdb.
saveamberparm SUS sustiva.top sustiva.crd
savdpdb SUS sustiva.lpdb
Finished! You can now run MD on this weird molecule.

12. tutorial directory and links
All the files for this tutorial can be found on
The shell script AchamberSUS.sh will use the one file sustiva.pdb to do all of the above steps quickly and should be referenced to quickly see the commands needed.
delete.com will delete all of the files generate by this process and will allow you to start over again for practice.
A very well written tutorial on this process can also be found on the net at: