As in the description on using MMPBSA , do I need to solvate the solute of
interest in explicit water after using default PBradii or can I solvate
this in other explicit solvent. Will I get more accurate results using PB
implicit solvent models.
Can you suggest something about this.
Thank You
Kirtana
On Tue, Oct 14, 2014 at 12:53 AM, kirtana S <skirtana4.gmail.com> wrote:
> As I understand to calculate the solvation energy I have to use PBSA to
> calculate the polar solvation energy. To estimate the non-polar part of
> solvation energy I have to use SASA + Vander Waals interaction energy
> between solute and solvent atoms.
> My question is about the type of files I will use to calculate this, i.e
> the prmtop and inpcrd file. Do I need to solvate it or use continuum
> solvent model.
>
> Regards
> Kirtana
>
> On Sun, Oct 12, 2014 at 4:44 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Sun, Oct 12, 2014, kirtana S wrote:
>> >
>> > Thank you. I do not want to use this information for any other purpose.
>> My
>> > main purpose is to obtain the solvation free energy. Do I need to set
>> up a
>> > simulation in implicit solvent conditions.There were some issues
>> related to
>> > running PB calculations as the dihedral phase was zero. Can you suggest
>> me
>> > other alternatives.
>>
>> You should report what the "dihedral phase was zero" problem was in
>> detail.
>> This should have nothing to do with PB calculations.
>>
>> My *guess* is that PB solvation with the simple version of non-polar
>> solvation is likely to give the most interpretable results. Since there
>> are no relevant experiments, there is no good indication that I know of
>> concerning how accurate one should expect the result to be.
>>
>> ....dac
>>
>>
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>
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Received on Mon Oct 13 2014 - 22:30:02 PDT
