Hi
you will have to set system for both ligand only and ligand-protein complex
also
Follow:-
http://ambermd.org/tutorials/advanced/tutorial9/#overview
thanks
Sadaf
On Tue, Oct 22, 2019 at 6:51 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> 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.
>
> Thanks
>
>
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Received on Tue Oct 22 2019 - 11:30:02 PDT
