On Wed, 2014-05-14 at 18:21 +0800, Ying-Chieh Sun wrote:
> Hi,
>
>
>
> We are learning TI computation for protein-ligand binding using pmemd of
> amber14. We used 3-step protocol ((1)switch charge off, (2) vdw
> transformation, (3)switch charge back on) to compute Delta Delta G of two
> ligand binding with the same protein.
>
>
>
> The results of the vdw transformation are summarized below:
>
>
>
> Delta G (Complex) Delta G(Solution)
>
> -1.6746+-4.7307 -0.4455+-4.0797 (pmemd of amber14: ligand charge: BCC
> charge!)
>
> -10.8895+-6.0608 -13.1352+-5.4417 (sander of amber11: ligand charge: RESP
> charge!)
>
>
>
> Because we used BCC charge this time for pmemd, we have not used RESP charge
> yet. But, in the vdw transformation, the charges are off. Therefore, I think
> the Delta G (not Delta Delta G) should be similar. But they differ by ~10
> kcal/mol in the complex and solution computations, respectively. The Delta
> Delta G’s are indeed in the similar range.
The TI code in pmemd is quite new and using it is radically different
than using the TI code in sander. Therefore, I would suggest changing
as _few_ things as possible when carrying out your comparisons. (i.e.,
make sure you are using exactly the same parameters in both cases to
carry out your simulations for comparison). Any attempt to explain the
discrepancy will most likely be unsubstantiated speculation.
>
>
>
> Any advice/suggestions are appreciated.
>
>
>
> We also found a typo, I think, in the output file. As shown below, it should
> be “A V E R A G E S O V E R 600000 S T E P S” instead of 3000 S T E P
> S.
No, this is correct. pmemd does not compute the energy every step (it
only computes the energy on the steps that it needs to print the
energy). This is done because computing the energy introduces an
unnecessary computational cost (and if you don't need the energy, why
compute it?). So my guess is that you printed every 200 steps for
600,000 total steps...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 14 2014 - 05:00:03 PDT
