[AMBER] Prmtop file creation for thermodynamic integration

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Tue, 22 Oct 2019 17:50:56 +0000

Dear Amber users,

I am at the very first step of setting up a TI setup for a kinase protein and a small molecule ligand (ligand has 10 atoms)

Page 422 of Amber18 manual says, in pmemd setup, there is only 1 prmtop file which should contain the atoms corresponding to both the start and the end steps.

Now, in my case, as I am trying to evaluate the absolute binding free energy of my ligand to the protein, I am essentially trying to simulate two steps State 1 : Ligand X (my ligand) fully exists in protein cavity; Step 2:Ligand X
 has disappeared.

Now should I have 2 copies of Ligand X in my complex.pdb file or should I have just 1 ligand X in my pdb file.
Can anyone help me in modifying the tleap.in file so that I can setup my TI runs. Please!

Here is my tleap.in file in current stage

source leaprc.gaff2
source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadOff atomic_ions.lib
loadOff solvents.lib
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
loadamberprep AUX.prepi
loadamberparams AUX.frcmod
pro=loadpdb minimized.pdb
solvatebox pro TIP3PBOX 12
charge pro
addions pro Na+ 0
savepdb pro complex_WAT_box.pdb
saveamberparm pro complex_WAT.prmtop complex_WAT.inpcrd
My minimized.pdb has 286 residues (protein) and 1 ligand X having 10 atoms.


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Received on Tue Oct 22 2019 - 11:00:02 PDT
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