Re: [AMBER] solvation free energy

From: kirtana S <>
Date: Tue, 14 Oct 2014 01:07:27 -0400

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

On Tue, Oct 14, 2014 at 12:53 AM, kirtana S <> 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 <>
> 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
>> _______________________________________________
>> AMBER mailing list
AMBER mailing list
Received on Mon Oct 13 2014 - 22:30:02 PDT
Custom Search