Classroom: Amber generate topology files and coordinate files

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Classroom: Amber generate topology files and coordinate files

2021-11-25 14:41:08 29 ℃

Amber generates topology files and coordinate files:

The coordinate file records the three-dimensional coordinates of all atoms in the simulation system.

Topology file records atomic connection relationship and molecular mechanical parameters.

The PDB file is required to be converted into topology files and coordinate files.

Tools you need LeAP:

TLLAP: Pure command line operation.

XLEAP: Graphical interface.

TLLAP operation:

Log in to the SCC host.

Enter the command tleap.

You can also enter the tleap -f file name for reading the necessary molecular power field parameter file.

Source Leaprc.proteins.ff03.r1 (Reading AMBER03 Battram) for processing macromolecules)

Source Leparc.glycam_06J-1 (read into the Glycam force field parameters, used to handle the power field of cyclodextrin)

Source Leaprc.gaff

Mol = loadingmol2 ***. Mol2 (read into small molecule template)

Loadamberparams *** MOD (read into small molecule template supplemental parameters)

List (you can display Unit read in LEAP)

COM = loadingpdb ***. PDB (readable after reading)

Saveamberparm COM Com.prmtop Com.inpcrd (Save Complex Topology Documents and Coordinate Files)

Adds COM Na + 0 (adding counter ions to the complex, maintain analog system electrical neutrality)

SolvateOct COM TIP3PBOX 12 (adding a cycle border solvent box for complex octaves)

SaveamberParm Cmp.prmtop Cmp.inpcrd (Save the complex topology document and coordinate document of the counter ion and solvent box)

Saveamberparm Mol Lig.prmtop Lig.inpcrd (Save Small Topology Document and Coordinate File)

In addition, you also need to read and save the topology document coordinate file of the protein.


Open with Pymol View: The Latom Name Displays the name to modify your own, so that your own is consistent with the Amber naming rule.

TLLAP (entering to the leap)

Source LeaPrc.protein.ff03.r1 (Reading Amber 03 Force Parameters, Used to Hand Molecules)


COM = loadingpdb ala7.pdb (COM: Molecular name, ALA7.PDB is file name,: assignment).

Bond com.7.o4 com.1.c1 (11th residue O4 is connected to the first residue C1) (O4 in com.7.o is atomic name, 7 is a residue name, COM is a molecular name) .

SaveamBerparm COM Com.prmtop Com.inpcrd (saved COM into COM.prmtop) and COM.INPCRD (coordinate file name)).

SolvateOct COM TIP3PBOX 12 (Solvent, OCT represents octahedron, COM represents the addition of COM molecules, TIP3PBOX means a water box, 12 indicates that the BOX thickness is 12å).

Saveamberparm com.prmtop com.inpcrd.


LL (display file size).

CD PBSA (to the PBSA directory).

MKDIR MD (create a new directory).

CD MD (in CD)


mv ../pdb/*.prmtop ./ (moving ../pdb/*.prmtop to the current folder) (* means no matter how many bits, no matter what character).

mv ../pdb/*.inpcrd. / Moves ../pdb/*.inpcrd to the current folder) (* means no matter how much, no matter what character).

Cp ../in/*.in. / Copy the in file).

Cp ../sn/*. / Copy the SH file).


Nohup sh & (sh min) MIN.SH, & indicates that this window can do other, NOHUP indicates that the program is running, which is independent of the window, that is, the window can be turned off and the program is still running).