Amber 10 Tutorial
antechamber: strange molecules get
parameter files
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.
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ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1 C1 SUS
2 H1 SUS
3 C2 SUS
4 C3 SUS
5 C4 SUS
6 C5 SUS
7 C6 SUS
8 H2 SUS
9 C7 SUS
10 H3 SUS
11 H4 SUS
12 C8 SUS
13 H5 SUS
14 H6 SUS
15 C9 SUS
16 F1 SUS
17 F2 SUS
18 F3 SUS
19 O1 SUS
20 C10 SUS
21 O2 SUS
22 N1 SUS
23 H7 SUS
24 C11 SUS
25 C12 SUS
26 H8 SUS
27 C13 SUS
28 H9 SUS
29 C14 SUS
30 Cl1 SUS
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sustiva.pdb
0.728 1.403 0.255
-0.136 1.756 0.782
0.803 0.080 -0.150
-0.290 -0.932 0.158
-1.635 -0.352 0.032
-2.718 0.123 -0.062
-4.044 0.695 -0.177
-4.741 0.335 0.558
-4.600 1.013 -1.541
-5.646 0.820 -1.697
-3.975 0.806 -2.390
-4.207 2.123 -0.629
-4.981 2.699 -0.155
-3.314 2.676 -0.858
-0.117 -1.500 1.582
1.056 -2.097 1.693
-0.170 -0.536 2.480
-1.047 -2.380 1.866
-0.232 -2.048 -0.712
0.893 -2.538 -1.245
0.922 -3.624 -1.713
1.964 -1.696 -1.242
2.776 -2.054 -1.692
1.919 -0.369 -0.836
2.963 0.503 -1.114
3.826 0.154 -1.653
2.892 1.817 -0.700
3.697 2.494 -0.911
1.772 2.262 -0.018
1.678 3.924 0.495
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.
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.
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*
8 ATOMTYPE.INF 4 sus.leap
4 ANTECHAMBER_AC.AC
4 delete.com* 92 sustiva.crd
4 ANTECHAMBER_AC.AC0
4 divcon.pdb 4 sustiva.frcmod
4 ANTECHAMBER_AM1BCC.AC
16 leap.log
4 sustiva.pdb
4 ANTECHAMBER_AM1BCC_PRE.AC 4 mopac.in
4 sustiva.prepin
4 ANTECHAMBER_BOND_TYPE.AC 40 mopac.out 376 sustiva.top
4 ANTECHAMBER_BOND_TYPE.AC0 4 mopac.pdb 164 sustivawh2o.lpdb
4 ANTECHAMBER_PREP.AC
4 NEWPDB.PDB
4 ANTECHAMBER_PREP.AC0
4 PREP.INF
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.
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.
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)
in LEAP
• now check if everything is o.k. with our SUS unit.
– check SUS
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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
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.
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
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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!
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.
tutorial directory and links
• All the files for this tutorial can be found on
saguaro@dnaseq:~/Quickgo/amber10tutorial/antechamber/
• 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:
http://hpce.iitm.ac.in/Manuals/Amber9_Tutorial/antechamber/ind
ex.htm