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
>>
>>
>>
>>
>>
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>>
>>
>
>
> --
> 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 - 07:30:03 PDT
