Yes, for #3 you will have to modify (i.e. make new) the protein.prmtop to
include the water molecule, also, if you are considering the water molecule
as part of the receptor. So you will need to create/use two new prmtop files
for this calculation.
-Bill
On Fri, May 6, 2011 at 10:21 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Bill
>
> Thank you very much. Indeed I used the original prmtop file. I have now
> stripped the Na+ ions. So the important thing is the 2nd question.
>
> As I mentioned, I've worked out the Delta G of the protein-ligand complex.
> Given that there's a HOH molecule in the binding site I want to work out its
> contribution to Delta G binding.
>
> For MMPBSA.py, I intend to use
>
> 1. complex_solvated.prmtop (original prmtop)
> 2. complex_HOH.prmtop (modified prmtop)
> 3. protein.prmtop (original prmtop)
> 4. ligand.prmtop (original prmtop)
>
>
>
> For 2 above, my intention is to generate a prmtop file from the a pdb file
> of the type:
>
> ATOM 2206 OXT TYR 141 20.064 34.883 10.511 0.00 0.00
> TER 0 0
> ATOM 2207 C1 LIG 142 13.612 30.103 24.510 0.00 0.00
> TER 0 0
> ATOM 2254 O WAT 143 13.139 20.066 151.222 0.00 0.00
>
> For 3, I though of using the original protein.prmtop but I'm not sure if I
> have to modify this to include HOH.
>
> Am I totally of the mark?
>
> Thank you very much for the advice
>
> George
>
>
> On May 6, 2011, at 1:38 PM, Bill Miller III wrote:
>
> > Your visualization problem appears to be because you are not loading a
> > corresponding prmtop file with the proper number of atoms. What prmtop
> did
> > you use alongside the 2nsHOH.mdcrd? You should be using a prmtop that
> only
> > contains the protein, ligand, single water molecule, and 13 Na+ atoms,
> since
> > those are the atoms in your mdcrd. It appears as if you are using a
> prmtop
> > that contains more than one water molecule. Did you intend to leave the
> Na+
> > atoms in the mdcrd? In general, it is not usually advised to use explicit
> > ions in MM-PBSA calculations. You might want to remove all the sodium
> ions
> > from the trajectory prior to running your closest.in file in ptraj.
> >
> > To answer your second question, you should be able to use any of the 200
> pdb
> > files that were created to generate your new complex/receptor/ligand
> prmtop
> > files since the exact coordinates do not matter. Just make sure to divide
> up
> > the respective prmtop files exactly as you intend for them to be divided
> > (i.e. will the water molecule be the ligand? included with the receptor?
> > included with the small organic molecule as part of the ligand? The
> answer
> > to these questions will depend on what question you want to answer by
> > performing the MM-PBSA calculation).
> >
> > I hope that helps.
> >
> > -Bill
> >
> > On Fri, May 6, 2011 at 6:30 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi everybody,
> >>
> >> I'm trying to work out the contribution of a buried water molecule to
> the
> >> Delta G of binding of a small organic molecule to a protein of 141
> residues.
> >>
> >> Based on earlier mailings to the list, I tried the following:
> >>
> >> 1. A test run to generate pdb files from my 2ns trajectory.
> >>
> >> Used: ptraj my.prmtop closest.in
> >>
> >> where <closest.in> was
> >>
> >> trajin 2ns.mdcrd
> >> trajout test.pdb pdb
> >> closest 1 :1-142 first
> >>
> >> The output was
> >> 1> CLOSESTWATERS: saving the 1 closest solvent molecules around atoms
> >> :1-142
> >> The current solvent mask is :155-8445
> >>
> >>
> >> PTRAJ: Successfully read in 200 sets and processed 200 sets.
> >>
> >> The output was 200 pdb files of the complex with 13 Na+ atoms and one
> water
> >> molecule.
> >>
> >> 2. Generated the processed trajectory
> >>
> >> Used: ptraj my.prmtop process.in
> >>
> >> where <process.in> was
> >>
> >> trajin 2ns.mdcrd
> >> trajout 2nsHOH.mdcrd
> >> closest 1 :1-142 first
> >>
> >> The visualisation of the 2nsHOH.mdcrd output is rather weird. I'm
> attaching
> >> a snapshot
> >>
> >> It shows the closest HOH molecules clustered around the complex and the
> Na+
> >> ions localised as a cluster around a specific part of the complex.
> >>
> >> I'm pretty sure this is not what I'm supposed to deal with. So there's
> >> something wrong with the above syntax.
> >>
> >> Could anyone please offer some suggestions.
> >>
> >> You're help is much appreciated.
> >>
> >> And a second related question.
> >>
> >> MMPBSA.py will require a new topology file (protein/ligand/water). To
> >> generate this topology file one would need a starting pdb. Can one use
> any
> >> pdb of the 200 generated in step 1 above?
> >>
> >> Thanks again
> >>
> >> George
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri May 06 2011 - 07:30:04 PDT
