Building molecules with tleap

In order to build PDB structures from sequence one may use programs like LEaP, included with Ambertools. The example below corresponds to the specific case of an acetylated and amidated alanine pentapeptide.

We start by starting LEaP, which in this specific case was installed through ananconda

$> tleap
-I: Adding /Users/.../anaconda3/dat/leap/prep to search path.
-I: Adding /Users/.../anaconda3/dat/leap/lib to search path.
-I: Adding /Users/.../anaconda3/dat/leap/parm to search path.
-I: Adding /Users/.../anaconda3/dat/leap/cmd to search path.

    Welcome to LEaP!
(no leaprc in search path)

This will leave a prompt for you to type a series of commands. Next we define the sequence of the peptide

> source leaprc.protein.ff14SBonlysc

----- Source: /Users/.../anaconda3/dat/leap/cmd/leaprc.protein.ff14SBonlysc
----- Source of /Users/.../anaconda3/dat/leap/cmd/leaprc.protein.ff14SBonlysc done
Log file: ./leap.log
Loading parameters: /Users/.../anaconda3/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /Users/.../anaconda3/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading parameters: /Users/.../anaconda3/dat/leap/parm/frcmod.ff99SB14
Reading force field modification type file (frcmod)
Reading title:
ff99SB backbone parameters (Hornak & Simmerling) with ff14SB atom types
Loading library: /Users/.../anaconda3/dat/leap/lib/amino12.lib
Loading library: /Users/.../anaconda3/dat/leap/lib/aminoct12.lib
Loading library: /Users/.../anaconda3/dat/leap/lib/aminont12.lib

Then we specify the sequence and whether we want to define a helical conformation.

> ala5 = sequence {ACE ALA ALA ALA ALA ALA NHE}
> impose ala5 { 1 2 3 4 5 } {{ "N" "CA" "C" "N" -40} {"C" "N" "CA" "C" -60}}

Finally, we can save the structure to a PDB file

> savepdb ala5 ala5.pdb
Writing pdb file: ala5.pdb

Adding D-amino acids to proteins

Following the example shown above, lets consider that the 2nd ALA is a D-amino acid rather than the defaul L-amino acid. In order to add the D-amino acid, after the sequence is built, we flip the selected residue. To do so, we define the sequence name, ala5 in this case, number of residue to flip and the atom we want to flip CA. Lastly, we flip the selected amino acid as shown below:

select ala5.2.CA
flip ala5

then, we continue as described above.

Building a topology file

Having built (or downloaded from the internet) a PDB file, we can proceed to generate other files required to run a simulation in Amber. Instead of invoking commands one by one, we can write an input file for LEaP Open your text editor and write the following

#tleap.in
source leaprc.protein.ff19SB
source leaprc.water.opc
ala5=loadpdb ala5.amber.pdb
SaveAmberParm ala5 ala5_gas.prmtop ala5_gas.inpcrd
solvateOct ala5 OPCBOX 5.0
addIonsRand ala5 Na+ 10 Cl- 10
SaveAmberParm ala5 ala5_solv.prmtop ala5_solv.inpcrd

Now save it as tleap.inp. Then, we can run the following command in the command line

$ tleap -f tleap.inp

This will result in a fully solvated simulation box. You may want to save it as a PDB file. In order to do this, you can run a write an input file for cpptraj. Use your text editor to write the following

trajin ala5_solv.inpcrd
trajout ala5_water.pdb PDB
run

and save it as pdb.inp. Now run

$ cpptraj -p ala5_solv.prmtop -i pdb.inp

For more details, check the official documentation of Amber here.