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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> 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 - 05:00:03 PDT
