Admin: Created page with " = Introduction = [http://ambermd.org/antechamber/antechamber.html Antechamber Online Manual] == Antechamber in Amber == File:Amber_flowchart.png File:hivrt.jpg *Cartesian coordinates for each atom in the system. These usually come from Xray crystallography, NMR spectroscopy, or model-building. They should be in Protein Databank (PDB) or Tripos "mol2" format. The program LEaP provides a platform for carrying out many of these modeling tasks, but users may..."

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Created page with " = Introduction = [http://ambermd.org/antechamber/antechamber.html Antechamber Online Manual] == Antechamber in Amber == File:Amber_flowchart.png File:hivrt.jpg *Cartesian coordinates for each atom in the system. These usually come from Xray crystallography, NMR spectroscopy, or model-building. They should be in Protein Databank (PDB) or Tripos "mol2" format. The program LEaP provides a platform for carrying out many of these modeling tasks, but users may..."

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= Introduction =
[http://ambermd.org/antechamber/antechamber.html Antechamber Online Manual]

== Antechamber in Amber ==
[[File:Amber_flowchart.png]] [[File:hivrt.jpg]]
*Cartesian coordinates for each atom in the system. These usually come from Xray crystallography, NMR spectroscopy, or model-building. They should be in Protein Databank (PDB) or Tripos "mol2" format. The program LEaP provides a platform for carrying out many of these modeling tasks, but users may wish to consider other programs as well.
*"Topology": connectivity, atom names, atom types, residue names, and charges. This information comes from the database, which is found in the amber9/dat/leap/prep directory. It contains topology for the standard amino acids as well as N- and C-terminal charged amino acids, DNA, RNA, and common sugars. The database contains default internal coordinates for these monomer units, but coordinate information is usually obtained from PDB files. Topology information for other molecules (not found in the standard database) is kept in user-generated "residue files", which are generally created using antechamber.
*Force field: Parameters for all of the bonds, angles, dihedrals, and atom types in the system. The standard parameters for several force fields are found in the amber9/dat/leap/parm directory

== General Amber Force Field (GAFF): ==
*Developed for general ligands
*Compatible with the AMBER force field
*Function form:
[[File:function.png|480px]]

*Bond/Angle/Dihedral Parameterizations
**Experimental Data and high level ab initio calculations
*Atom types:
**lower case, covers the organic chemical space
*Charge approach: RESP or AM1-BCC

=== What can Antechamber do? ===
*Needed for non-standard residues
*Assign atom types from GAFF
*Generate empirical/semiempirical charges
**AM1-BCC, Mulliken, Gasteiger…
*Extract QM charges from output
**Gaussian and Jaguar outputs
*Prepare input mol2 file for leap
**Convert different file formats to mol2 file
*File Conversions
[[File:conversion.png|640px]]
*For simple molecules:
**Define a topology
*Use Antechamber to:
**Choose atom types
**Calculate a set of partial charges
**Generate forcefield parameters
*Use Leap to:
**Create a new residue library
**Define a topology

tleap (terminal LEaP) is the non-graphical, command-line-only interface to LEaP. It has the
same functionality as the xleap main window (Universe Editor Command Window, described
below), and uses standard text control keys.

xleap is a windowing interface to LEaP. In addition to the command-line interface contained in the Universe
Editor window, it has a Unit Editor (graphical molecule editor), an Atom Properties Editor, and a Parmset Editor.

*Extract it from an existing pdb
**Search from http://www.rcsb.org/pdb/home/home.do
**Add hydrogens using “reduce”
**Build it from any molecular builder
***xleap, chimera, maestro, etc.
**Save as pdb and visualize
[[File:susa.png|240px]]

=== Choose atom types from GAFF ===
[[File:atom type.png|540px]]

=== Assign partial charges ===

[[File:charge.png|540px]]

=== Determine Partial Charges ===
*RESP Charges
**RESP Charges
**Fit point charges to potential
**Equal charges for topologically equivalent atoms
**Requires QM programs (Gaussian, Gamess, Jaguar, etc)
*AM1-BCC Charges
**Fast, empirical generation
**Emulate RESP charges
**Can be directly generated from antechamber
Bayly, C.I., Cieplak, P., Cornell, W., Kollman, P.A., J Phys Chem B., 97, 10269, 1993.
Jakalian, A., Bush, B.L, Jack, D.B., Bayly, C.I., J Comput Chem, 21, 132, 2000.

Gaussian otimization is different for amberff99 and amber03.

*For ff99SB and ff99:

Quantum chemical calculations were executed for the small ligand to deduce the atom charges
utilized in MD simulations.Geometry optimization was performed on each ligand, and the electrostatic
potential was calculated at the HF/6-31G(d) level using the Gaussian03 program. The partial atom
charges were determined using the RESP method.

antechamber -fi mol2 -fo gcrt -i *.mol2 -o *.com

#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
remark line goes here
0 1
Cl -2.5793 -35.3531 21.8877
F 3.1260 -39.5175 20.6374
F 1.2729 -39.1990 21.7451

*For ff03:

Quantum chemical calculations were executed for the ligand to deduce the atom charges utilized
in MD simulations. Geometry optimization was performed on ligand at the HF/6-31G(d,p) level, and
the electrostatic potential was calculated at the B3LYP/cc-pVTZ level under solvation conditions
with ether (ε = 4) by the IEFPCM method using the Gaussian 03 program. The partial atom charges
were determined using the RESP program, implemented in the AMBER9 package.

%chk=*.chk
%mem=20mw
#p opt(modredundant) rhf/6-31g(d,p) geom=connectivity scf=tight test pop=mk iop(6/33=2,6/42=6)

%chk=*.chk
%mem=100mw
#P B3LYP/cc-pvtz SCRF=(IEFPCM,Read) Geom=AllCheck Guess=Read Pop=(Minimal,MK) IOp(6/33=2,6/41=10,6/42=17)

=== Check forcefield parameters ===

*Check if there are missing parameters:
**Use the “check” command in leap
*Missing parameters can be:
**Generated using “parmchk” utility (Problematic parameters generates warnings:“Attn, need revision.” )

=== Generate force field parameters ===
[[File:force2.png|640px]]

=== Build a library file ===
*Completely defines a molecule in AMBER terms
*Includes information on atom names, types, charges and topology
[[File:library1.png|640px]]

=== Use your new residue ===

[[File:newresidue.png|640px]]

=== When running Antechamber, Make Sure that … ===
*Your pdb file has the correct geometry and connectivity.
*The atom names in your molecule are unique.
*Your molecule does not have open valence.
*The correct net charge of your molecule is specified.
*The atom names and residue name of the coordinates. match the created library file.

=== Where to find predefined libraries:The contributed parameter database ===
*Check here first:
http://www.pharmacy.manchester.ac.uk/bryce/amber
*Cofactors: GDP, GTP, ADP, ATP, FADH, NADH, NADPH
*Lipids: DMPC, DOPC
*Ions, organic molecules, modified AAs…

=== How to derive RESP charges: Use of R.E.D ===
*RESP ESP Charge Derive
**Check this:http://q4md-forcefieldtools.org/RED/
*Database with RESP-charged mol2 files:
**http://q4md-forcefieldtools.org/REDDB/index.php
**Organic solvent: acetonitrile, benzene, toluene, etc.
**New AA/RNA/DNA fragments…
*Server for deriving new RESP/ESP charges.
*Automated procedure for RESP fitting.

= Case study =

*Sustiva:http://www.sustiva.com/

[[Image:Sus1.png|300px]]

*Sustiva is a human immunodeficiency virus type 1 (HIV-1) specific, non-nucleoside, reverse transcriptase inhibitor marketed by Bristol Myers Squibb for controlling the progression of HIV infection in humans. The chemical name for Sustiva is (S)-6-chloro-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one.
*Here is a basic 3 dimensional geometry for Sustiva from which we will start to build our topology and coordinate files from sustiva.pdb.

REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EFZ A 999
HETATM 7759 CL EFZ A 999 -4.685 -32.725 25.222 1.00 50.93 CL
HETATM 7760 F1 EFZ A 999 -0.755 -36.632 25.697 1.00 62.80 F
HETATM 7761 F2 EFZ A 999 1.078 -37.043 24.672 1.00 70.73 F
HETATM 7762 F3 EFZ A 999 -0.784 -37.177 23.626 1.00 75.12 F
HETATM 7763 O1 EFZ A 999 1.524 -34.934 20.910 1.00 73.73 O
HETATM 7764 O2 EFZ A 999 0.989 -34.880 23.058 1.00 73.24 O
HETATM 7765 N EFZ A 999 -0.681 -34.971 21.434 1.00 71.12 N
HETATM 7766 C1 EFZ A 999 -1.662 -34.414 22.313 1.00 71.29 C
HETATM 7767 C2 EFZ A 999 -2.915 -33.947 21.843 1.00 72.17 C
HETATM 7768 C3 EFZ A 999 -3.838 -33.423 22.771 1.00 71.25 C
HETATM 7769 C4 EFZ A 999 -3.533 -33.373 24.119 1.00 63.88 C
HETATM 7770 C5 EFZ A 999 -2.310 -33.829 24.593 1.00 63.40 C
HETATM 7771 C6 EFZ A 999 -1.386 -34.378 23.681 1.00 68.96 C
HETATM 7772 C7 EFZ A 999 -0.002 -34.957 24.144 1.00 71.35 C
HETATM 7773 C8 EFZ A 999 0.552 -34.236 25.315 1.00 75.97 C
HETATM 7774 C9 EFZ A 999 0.985 -33.657 26.241 1.00 81.31 C
HETATM 7775 C10 EFZ A 999 1.605 -32.802 27.586 1.00 80.51 C
HETATM 7776 C11 EFZ A 999 2.808 -33.083 27.639 1.00 83.59 C
HETATM 7777 C12 EFZ A 999 2.404 -31.980 27.123 1.00 79.58 C
HETATM 7778 C13 EFZ A 999 -0.121 -36.472 24.539 1.00 72.76 C
HETATM 7779 C14 EFZ A 999 0.665 -34.932 21.725 1.00 70.58 C
TER
END

Our Sustiva pdb file is extracted from the RT-sustiva complex pdb file (pdb code : 1FKO.pdb, http://www.rcsb.org/pdb/explore/explore.do?structureId=1FKO). The coordinates of sustiva is associated with a residue called "EFZ" (Efavirenz). By all means open it up in PyMol and take a look at it.

[[Image:Fko.png|200px]]

*Create parameter and coordinate files for Sustiva run AMBER reduce to add all the hydrogen atoms to the pdb file. The hydrogenated sustiva coordinate can be found in sustiva_h.pdb

USER MOD reduce.3.13.080428 H: found=0, std=0, add=9, rem=0, adj=0
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EFZ A 999
HETATM 7759 CL EFZ A 999 -4.685 -32.725 25.222 1.00 50.93 CL
HETATM 7760 F1 EFZ A 999 -0.755 -36.632 25.697 1.00 62.80 F
HETATM 7761 F2 EFZ A 999 1.078 -37.043 24.672 1.00 70.73 F
HETATM 7762 F3 EFZ A 999 -0.784 -37.177 23.626 1.00 75.12 F
HETATM 7763 O1 EFZ A 999 1.524 -34.934 20.910 1.00 73.73 O
HETATM 7764 O2 EFZ A 999 0.989 -34.880 23.058 1.00 73.24 O
HETATM 7765 N EFZ A 999 -0.681 -34.971 21.434 1.00 71.12 N
HETATM 7766 C1 EFZ A 999 -1.662 -34.414 22.313 1.00 71.29 C
HETATM 7767 C2 EFZ A 999 -2.915 -33.947 21.843 1.00 72.17 C
HETATM 7768 C3 EFZ A 999 -3.838 -33.423 22.771 1.00 71.25 C
HETATM 7769 C4 EFZ A 999 -3.533 -33.373 24.119 1.00 63.88 C
HETATM 7770 C5 EFZ A 999 -2.310 -33.829 24.593 1.00 63.40 C
HETATM 7771 C6 EFZ A 999 -1.386 -34.378 23.681 1.00 68.96 C
HETATM 7772 C7 EFZ A 999 -0.002 -34.957 24.144 1.00 71.35 C
HETATM 7773 C8 EFZ A 999 0.552 -34.236 25.315 1.00 75.97 C
HETATM 7774 C9 EFZ A 999 0.985 -33.657 26.241 1.00 81.31 C
HETATM 7775 C10 EFZ A 999 1.605 -32.802 27.586 1.00 80.51 C
HETATM 7776 C11 EFZ A 999 2.808 -33.083 27.639 1.00 83.59 C
HETATM 7777 C12 EFZ A 999 2.404 -31.980 27.123 1.00 79.58 C
HETATM 7778 C13 EFZ A 999 -0.121 -36.472 24.539 1.00 72.76 C
HETATM 7779 C14 EFZ A 999 0.665 -34.932 21.725 1.00 70.58 C
HETATM 0 H122 EFZ A 999 2.472 -31.798 26.040 1.00 79.58 H new
HETATM 0 H121 EFZ A 999 2.585 -31.017 27.623 1.00 79.58 H new
HETATM 0 H112 EFZ A 999 3.348 -33.100 28.597 1.00 83.59 H new
HETATM 0 H111 EFZ A 999 3.235 -33.882 27.015 1.00 83.59 H new
HETATM 0 H101 EFZ A 999 0.784 -32.761 28.317 1.00 80.51 H new
HETATM 0 HN EFZ A 999 -0.981 -35.402 20.583 1.00 71.12 H new
HETATM 0 H5 EFZ A 999 -2.066 -33.763 25.664 1.00 63.40 H new
HETATM 0 H3 EFZ A 999 -4.811 -33.050 22.419 1.00 71.25 H new
HETATM 0 H2 EFZ A 999 -3.163 -33.993 20.772 1.00 72.17 H new
TER
END

$AMBERHOME/exe/reduce sustiva.pdb > sustiva_h.pdb

*Change the name of the residue from "EFZ" to "SUS", and create a new pdb file: sus_new.pdb

USER MOD reduce.3.13.080428 H: found=0, std=0, add=9, rem=0, adj=0
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SUS A 999
HETATM 7759 CL SUS A 999 -4.685 -32.725 25.222 1.00 50.93 CL
HETATM 7760 F1 SUS A 999 -0.755 -36.632 25.697 1.00 62.80 F
HETATM 7761 F2 SUS A 999 1.078 -37.043 24.672 1.00 70.73 F
HETATM 7762 F3 SUS A 999 -0.784 -37.177 23.626 1.00 75.12 F
HETATM 7763 O1 SUS A 999 1.524 -34.934 20.910 1.00 73.73 O
HETATM 7764 O2 SUS A 999 0.989 -34.880 23.058 1.00 73.24 O
HETATM 7765 N SUS A 999 -0.681 -34.971 21.434 1.00 71.12 N
HETATM 7766 C1 SUS A 999 -1.662 -34.414 22.313 1.00 71.29 C
HETATM 7767 C2 SUS A 999 -2.915 -33.947 21.843 1.00 72.17 C
HETATM 7768 C3 SUS A 999 -3.838 -33.423 22.771 1.00 71.25 C
HETATM 7769 C4 SUS A 999 -3.533 -33.373 24.119 1.00 63.88 C
HETATM 7770 C5 SUS A 999 -2.310 -33.829 24.593 1.00 63.40 C
HETATM 7771 C6 SUS A 999 -1.386 -34.378 23.681 1.00 68.96 C
HETATM 7772 C7 SUS A 999 -0.002 -34.957 24.144 1.00 71.35 C
HETATM 7773 C8 SUS A 999 0.552 -34.236 25.315 1.00 75.97 C
HETATM 7774 C9 SUS A 999 0.985 -33.657 26.241 1.00 81.31 C
HETATM 7775 C10 SUS A 999 1.605 -32.802 27.586 1.00 80.51 C
HETATM 7776 C11 SUS A 999 2.808 -33.083 27.639 1.00 83.59 C
HETATM 7777 C12 SUS A 999 2.404 -31.980 27.123 1.00 79.58 C
HETATM 7778 C13 SUS A 999 -0.121 -36.472 24.539 1.00 72.76 C
HETATM 7779 C14 SUS A 999 0.665 -34.932 21.725 1.00 70.58 C
HETATM 0 H122 SUS A 999 2.472 -31.798 26.040 1.00 79.58 H new
HETATM 0 H121 SUS A 999 2.585 -31.017 27.623 1.00 79.58 H new
HETATM 0 H112 SUS A 999 3.348 -33.100 28.597 1.00 83.59 H new
HETATM 0 H111 SUS A 999 3.235 -33.882 27.015 1.00 83.59 H new
HETATM 0 H101 SUS A 999 0.784 -32.761 28.317 1.00 80.51 H new
HETATM 0 HN SUS A 999 -0.981 -35.402 20.583 1.00 71.12 H new
HETATM 0 H5 SUS A 999 -2.066 -33.763 25.664 1.00 63.40 H new
HETATM 0 H3 SUS A 999 -4.811 -33.050 22.419 1.00 71.25 H new
HETATM 0 H2 SUS A 999 -3.163 -33.993 20.772 1.00 72.17 H new
TER
END

*Create the "mol2" file, required to define a new unit in leap, we simply run the following command:

$AMBERHOME/exe/antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2

*The screen output should be as follows:

Running: /usr/local/amber10/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /usr/local/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 160; net charge: 0
Running: /usr/local/amber10/bin/mopac.sh
Running: /usr/local/amber10/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/usr/local/amber10/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /usr/local/amber10/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

*Get a whole series of files written to your directory

ANTECHAMBER_AC.AC ANTECHAMBER_AM1BCC_PRE.AC ATOMTYPE.INF mopac.out sustiva.mol2ANTECHAMBER_AC.AC0
ANTECHAMBER_BOND_TYPE.AC divcon.pdb mopac.pdb sustiva.pdb ANTECHAMBER_AM1BCC.AC ANTECHAMBER_BOND_TYPE.AC
mopac.in

The files in CAPITALS are all intermediate files used by antechamber and are not required here.

The file that we are really interested in, and the reason we ran Antechamber in the first place, is the sustiva.mol2 file. This contains the definition of our sustiva residue including all of the charges and atom types that we will load into Leap to when creating our prmtop and inpcrd files. Let's take a quick look at the file:

'''''IMPORTANT: make sure the second line here is the res/lib name SUS, which should match the load, lib name below.'''''

@<TRIPOS>MOLECULE
SUS
30 32 1 0 0
SMALL
bcc
@<TRIPOS>ATOM
1 CL -4.6850 -32.7250 25.2220 cl 999 SUS -0.073100
2 F1 -0.7550 -36.6320 25.6970 f 999 SUS -0.231400
3 F2 1.0780 -37.0430 24.6720 f 999 SUS -0.221400
4 F3 -0.7840 -37.1770 23.6260 f 999 SUS -0.216800
5 O1 1.5240 -34.9340 20.9100 o 999 SUS -0.573600
6 O2 0.9890 -34.8800 23.0580 os 999 SUS -0.371900
7 N -0.6810 -34.9710 21.4340 n 999 SUS -0.459500
8 C1 -1.6620 -34.4140 22.3130 ca 999 SUS 0.084700
9 C2 -2.9150 -33.9470 21.8430 ca 999 SUS -0.167000
10 C3 -3.8380 -33.4230 22.7710 ca 999 SUS -0.069500
11 C4 -3.5330 -33.3730 24.1190 ca 999 SUS -0.025500
12 C5 -2.3100 -33.8290 24.5930 ca 999 SUS -0.040200
13 C6 -1.3860 -34.3780 23.6810 ca 999 SUS -0.163900
14 C7 -0.0020 -34.9570 24.1440 c3 999 SUS 0.315500
15 C8 0.5520 -34.2360 25.3150 c1 999 SUS -0.193300
16 C9 0.9850 -33.6570 26.2410 c1 999 SUS 0.012400
17 C10 1.6050 -32.8020 27.5860 cx 999 SUS -0.082700

SUS
30
-4.6850000 -32.7250000 25.2220000 -0.7550000 -36.6320000 25.6970000
1.0780000 -37.0430000 24.6720000 -0.7840000 -37.1770000 23.6260000
1.5240000 -34.9340000 20.9100000 0.9890000 -34.8800000 23.0580000
-0.6810000 -34.9710000 21.4340000 -1.6620000 -34.4140000 22.3130000
-2.9150000 -33.9470000 21.8430000 -3.8380000 -33.4230000 22.7710000
-3.5330000 -33.3730000 24.1190000 -2.3100000 -33.8290000 24.5930000
-1.3860000 -34.3780000 23.6810000 -0.0020000 -34.9570000 24.1440000
0.5520000 -34.2360000 25.3150000 0.9850000 -33.6570000 26.2410000
1.6050000 -32.8020000 27.5860000 2.8080000 -33.0830000 27.6390000
2.4040000 -31.9800000 27.1230000 -0.1210000 -36.4720000 24.5390000
0.6650000 -34.9320000 21.7250000 2.4720000 -31.7980000 26.0400000
2.5850000 -31.0170000 27.6230000 3.3480000 -33.1000000 28.5970000
3.2350000 -33.8820000 27.0150000 0.7840000 -32.7610000 28.3170000
-0.9810000 -35.4020000 20.5830000 -2.0660000 -33.7630000 25.6640000
-4.8110000 -33.0500000 22.4190000 -3.1630000 -33.9930000 20.7720000

We can use the utility parmchk to test if all the parameters we require are available.

$AMBERHOME/exe/parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod

Run this command now and it will produce a file called sustiva.frcmod. This is a parameter file that can be loaded into Leap in order to add missing parameters. Here it will contain all of the missing parameters. If it can antechamber will fill in these missing parameters by analogy to a similar parameter. You should check these parameters carefully before running a simulation. If antechamber can't empirically calculate a value or has no analogy it will either add a default value that it thinks is reasonable or alternatively insert a place holder (with zeros everywhere) and the comment "ATTN: needs revision". In this case you will have to manually parameterise this yourself. It is hope that as GAFF is developed so the number of missing parameters will decrease. Let's look at our frcmod file:

remark goes here
MASS
BOND
ANGLE
ca-c3-c1 64.784 110.735 Calculated with empirical approach
c1-c1-cx 56.400 177.990 same as c1-c1-c3
c1-cx-cx 64.200 111.590 same as c1-c3-c3
c1-cx-hc 48.300 109.750 same as c1-c3-hc
DIHE
IMPROPER
c -ca-n -hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default value
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
n -o -c -os 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
NONBON

We now have everything we need to load sustiva as a unit in Leap. We just need to load tLeap and ensure the GAFF force field is available. First, download an updated version of tleap

#!/bin/sh
$AMBERHOME/bin/teLeap \
-I$AMBERHOME/dat/leap/prep \
-I$AMBERHOME/dat/leap/lib \
-I$AMBERHOME/dat/leap/parm \
-I$AMBERHOME/dat/leap/cmd \
$*

$AMBERHOME/exe/tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

Load GAFF force field into tLeap with:

source leaprc.gaff

tLeap console should now look something like this:

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /usr/local/amber10/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
>

Load sustiva unit (sustiva.mol2):

SUS = loadmol2 sustiva.mol2

If you now type list in tLeap you should see the new SUS unit (highlighted in bold):

> SUS = loadmol2 sustiva.mol2
Loading Mol2 file: ./sustiva.mol2
Reading MOLECULE named SUS
> list
ACE ALA ARG ASH ASN ASP CALA CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX
CHID CHIE CHIP CHIS CILE CIO CLEU CLYS
CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL
CYM CYS CYX Cl- Cs+ DA DA3 DA5
DAN DC DC3 DC4 DC5 DCN DG DG3
DG5 DGN DT DT3 DT5 DTN GLH GLN
GLU GLY HID HIE HIP HIS HOH IB
ILE K+ LEU LYN LYS Li+ MEOHBOX MET
MG2 NALA NARG NASN NASP NCYS NCYX NGLN
NGLU NGLY NHE NHID NHIE NHIP NHIS NILE
NLEU NLYS NMABOX NME NMET NPHE NPRO NSER
NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX
PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3
RC5 RCN RG RG3 RG5 RGN RU RU3
RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF
SPG SUS T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX
TP3 TP4 TP5 TPF TRP TYR VAL WAT
frcmod99SBgaff parm99

At this point we haven't loaded the frcmod file that parmchk gave us. Thus if we check our SUS unit we should find that there are 4 missing angle type parameters.

check SUS

> 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
Could not find angle parameter: c1 - cx - cx
There are missing parameters.
Unit is OK.

loadamberparams sustiva.frcmod

> loadamberparams sustiva.frcmod
loading parameters: ./sustiva.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> check SUS
Checking 'SUS'....
Checking parameters for unit 'SUS'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.

We can now create the library file for sustiva (sus.lib)

!!index array str
"SUS"
!entry.SUS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"CL" "cl" 0 1 131072 1 6 -0.073100
"F1" "f" 0 1 131072 2 9 -0.231400
"F2" "f" 0 1 131072 3 9 -0.221400
"F3" "f" 0 1 131072 4 9 -0.216800
"O1" "o" 0 1 131072 5 8 -0.573600
"O2" "os" 0 1 131072 6 8 -0.371900
"N" "n" 0 1 131072 7 7 -0.459500
"C1" "ca" 0 1 131072 8 6 0.084700
"C2" "ca" 0 1 131072 9 6 -0.167000
"C3" "ca" 0 1 131072 10 6 -0.069500
"C4" "ca" 0 1 131072 11 6 -0.025500
"C5" "ca" 0 1 131072 12 6 -0.040200
"C6" "ca" 0 1 131072 13 6 -0.163900
"C7" "c3" 0 1 131072 14 6 0.315500
"C8" "c1" 0 1 131072 15 6 -0.193300
"C9" "c1" 0 1 131072 16 6 0.012400
"C10" "cx" 0 1 131072 17 6 -0.082700
"C11" "cx" 0 1 131072 18 6 -0.108400
"C12" "cx" 0 1 131072 19 6 -0.107700
"C13" "c3" 0 1 131072 20 6 0.609900
"C14" "c" 0 1 131072 21 6 0.824700
"H122" "hc" 0 1 131072 22 1 0.087500
"H121" "hc" 0 1 131072 23 1 0.077800
"H112" "hc" 0 1 131072 24 1 0.078200
"H111" "hc" 0 1 131072 25 1 0.087300
"H101" "hc" 0 1 131072 26 1 0.104300
"HN" "hn" 0 1 131072 27 1 0.344000
"H5" "ha" 0 1 131072 28 1 0.169400
"H3" "ha" 0 1 131072 29 1 0.156700
"H2" "ha" 0 1 131072 30 1 0.153700
!entry.SUS.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"CL" "cl" 0 -1 0.0
"F1" "f" 0 -1 0.0
"F2" "f" 0 -1 0.0
"F3" "f" 0 -1 0.0
"O1" "o" 0 -1 0.0
"O2" "os" 0 -1 0.0
"N" "n" 0 -1 0.0

saveoff SUS sus.lib

The output from tleap shows a few warnings, which can be safely ignored (in this case!) due to the triangular bond geometry of sustiva:

> saveoff SUS sus.lib
Building topology.
Building atom parameters.
>
> saveamberparm SUS sustiva.prmtop sustiva.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 7 12 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 7 9 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 9 12 duplicates bond ('triangular' bond) or angle ('square' bond)
Building improper torsion parameters.
total 8 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
SUS 1
)
(no restraints)
>

Instead of typing everything in the tleap console, the list of tLeap commands mentioned above can also be used to create a tLeap input file (tleap.in) and generate all the required files:

source leaprc.ff99SB
source leaprc.gaff
SUS = loadmol2 sustiva.mol2
check SUS
loadamberparams sustiva.frcmod
saveoff SUS sus.lib
#solvatebox mol TIP3PBOX 9.0
#charge mol
#addIons2 mol Na+ 0
saveamberparm SUS sustiva.prmtop sustiva.inpcrd
quit

$AMBERHOME/exe/tleap -f tleap.in

'''Creating topology and coordinate files for Sustiva-RT complex '''

Since we can mix the traditional AMBER force fields with GAFF, we can at this point load a fragment of the reverse transcriptase (RT) from HIV virus and treat this using the ff99SB force field while treating the Sustiva molecule using the GAFF force field. We will need to use the Sustiva library file (sus.lib) that was created in the previous step.

The RT-Sustiva complex can be found in the RCSB protein data bank (pdb code 1FKO). The corresponding pdb file is 1FKO.pdb.

HIV reverse transcriptase is a heterodimer composed of the p51 and p66 subunits. It is a large protein with a molecular mass of 117 kDa. For the purpose of this tutorial, we will use a truncated system in close proximity of Sustiva, including the finger and palm domains of the p66 subunit. The truncated pdb file is: 1FKO_trunc.pdb.

In order to have the 1FKO pdb file recognized by tLeap once the Sustiva library file is loaded, we need to change the residue name in the 1FKO pdb file from EFZ to SUS. Since the Sustiva libary file includes the same atom names as the Sustiva molecule in the 1FKO pdb file, no further modification is necessary. In other cases it is always a good idea to check the pdb file against the library file to make sure they have matching atom names as well as residue name. The modified pdb file is now: 1FKO_trunc_sus.pdb.

Now we are able to load the pdb file into tLeap.

First, we start tLeap just like what we did in the previous section:

$AMBERHOME/exe/tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>source leaprc.gaff
>loadamberparams sustiva.frcmod

Now we load the Sustiva library file (sus.lib), followed by the complex pdb file 1FKO_trunc_sus.pdb.

>loadoff sus.lib
>complex = loadpdb 1FKO_trunc_sus.pdb

Finally, we are ready to create our topology and coordinate files of the truncated RT-sustiva complex.

>saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd
>savepdb complex 1FKO_sus.pdb
>quit

You can take a look at the truncated RT-Sustiva complex structure (1FKO_sus.pdb) in VMD.

[[Image:RT.png|300px]]

<br>

Again we can create a tLeap input file (tleap.in) and generate all the files for the Sustiva-RT complex:

source leaprc.ff99SB
source leaprc.gaff
loadamberparams sustiva.frcmod
loadoff sus.lib
complex = loadpdb 1FKO_trunc_sus.pdb
saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd
savepdb complex 1FKO_sus.pdb
quit

Other useful commands include "solvate" or solvateoct, and addion2 (neutralize)

Ammm:Ff amber ligand parameter - Revision history