On Wed, Apr 2, 2014 at 10:57 AM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> Respected sir,
>
> I would like to explain the whole scenario.
>
>
> 1) I had two PDB files of same protein with different
> terminal residues let us give them name PDB1 and PDB2
> 2) PDB1 has about 30 residues less than PDB2
> 3) I ran MD simulation for both using same protocol
> 4) I stripped extra residues thus having similar number of
> residues in both.
> 5) However, as the PDB2 had extra residues the water
> molecules were different in the trajectory and prmtop files after stripping
> which can be seen from the a portion of .out files
> .....................................................
> ACTION SETUP FOR PARM [complex_solvated.prmtop] (1 actions):
> 0: [strip :1,151-154,Na+,Cl- outprefix stripped_PDB1]
> Stripping 74 atoms.
> Topology complex_solvated.prmtop contains 23467 atoms.
> 7149 residues.
> 23490 bonds.
> 7001 molecules.
> Box: Trunc. Oct.
> 6999 solvent molecules.
> Final solute residue is 150
> Writing out amber topology file complex_solvated.prmtop to
> stripped_PDB1.complex_solvated.prmtop
> .....................................................
> ACTION SETUP FOR PARM [complex_solvated.prmtop] (1 actions):
> 0: [strip :1-18,168-182,Na+,Cl- outprefix stripped_PDB2]
> Stripping 476 atoms.
> Topology complex_solvated.prmtop contains 42599 atoms.
> 13526 residues.
> 42622 bonds.
> 13378 molecules.
> Box: Trunc. Oct.
> 13376 solvent molecules.
> Final solute residue is 150
> Writing out amber topology file complex_solvated.prmtop to
> stripped_PDB2.complex_solvated.prmtop
>
> 6) Now, I want to merge the stripped trajectories and do
> analysis on final trajectory like clustering of ligand poses, binding free
> energy etc.
> 7) However, for that I need a prmtop file and which is the
> place I am stuck.
> 8) I thought that by stripping extra water from the PDB2
> prmtop and trajectory I can do the analysis.
>
> I hope you can get an idea what I am trying to achieve and guide me
> accordingly. Please do let me know if I need to change the approach as the
> main aim is to correlate the pose and binding free energy of the ligand
> with IC50 value. The other idea that comes to my mind is to use both
> trajectories separately and see if the results are same in both in terms of
> pose and binding free energy trend.
>
I would analyze them separately. 30 residues can make a huge difference
in the dynamics of the system.
Also, it doesn't seem like you're doing anything with the solvent. So why
not strip out all waters from both systems?
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 02 2014 - 08:30:03 PDT
