On Tue, Apr 9, 2013 at 9:29 PM, dbaogen <dbaogen.gmail.com> wrote:
> **
> Hi Jason,
>
> Thanks for your reply. The nonpolar solvation energies are
> -3.4672 and -31.1906 kcal/mol using " &pb istrng=0.1," in AmberTools 1.5and "
> &pb istrng=0.1, sander_apbs=1,radiopt=0", respectively.
>
> Does it mean that the nopolar solvation energies are both
> calculated by the equation G(np) = surften*SASA+offset in the above two
> cases according to your email? Thanks!
>
I believe so. The SASAs will be computed differently, though (and the
default surface tension term may be different, I'm not sure). But I do not
use sander.APBS regularly, so you should check the
_MMPBSA_complex_pb.mdout.0 file (and related files) to get more details.
All the best,
Jason
> Best wishes
> Duan Baogen
>
>
>
>
> *From:* Jason Swails <jason.swails.gmail.com>
> *Date:* 2013-04-10 05:56
> *To:* dbaogen <dbaogen.gmail.com>; AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] large difference of nonpolar solvation free energy
> using MMPBSA.py in AmberTools1.5 or AmberTools12
>
>
>
> On Tue, Apr 9, 2013 at 3:24 AM, dbaogen <dbaogen.gmail.com> wrote:
>
>> Dear all,
>>
>> I have met a problem in calculation binding free energy using
>> MMPBSA.py script in two versions of AmberTools. one is Amber 11 combined
>> with AmberTools 1.5. The nonpolar solvation energy (ECAVITY ) is -3.4672
>> kcal/mol. And the input file is as follow:
>>
>> MMPBSA input file for Amber 11 and AmberTools 1.5
>> &general
>> startframe=1, endframe=100, interval=1,
>> keep_files=0,strip_mdcrd=0,verbose=1,
>> /
>> &pb
>> istrng=0.1,
>> /
>> Searching in the AmberTools 1.5 Manual, the nonpolar solvation energy is
>> calculated by using the equation G(np) = SurfTen*SASA+SurOFF = G(cavity)
>> under the above parameter settings.
>>
>> The other is Amber 11 and AmberTools 12. The input file:
>>
>> MMPBSA input file for Amber 11 and AmberTools 12
>> &general
>> startframe=1, endframe=100, interval=1,
>> keep_files=2,search_path=1,verbose=1,
>> /
>> &pb
>> istrng=0.1, sander_apbs=1,radiopt=0
>> /
>> In this condition, according to the manual, the nonpolar solvation
>> free energy is calculated by using G(np)=G(disp)+G(cavity), and the value
>> (ENPOLAR) is -31.1906 kcal/mol. In addition, the AmberTools 12 manual
>> mentions that the default parameters must be INP=2 with radiopt =1.
>> whether did it mean that I set the wrong parameters for MMPBSA.py script?
>>
>
> This is not right, I don't think. The dispersion/cavitation decomposition
> of the non-polar solvation free energy is only available via the PBSA
> source code, _not_ via sander.APBS. Therefore, I think that the surface
> area term here is the simple term G(np) = surften*SASA+offset.
>
>>
>> If I changed the "radiopt" to 1, the error message is "CalcError:
>> sander.APBS failed with prmtop" when sander_apbs is set to 1. If the
>> parameter radiopt=1 and sander_apbs=0, the error message is " PB Bomb in
>> pb_aaradi(): No radius assigned for atom 3 C5' CI ". The program is
>> normally ended only when radiopt is set to 0.
>>
>
> You must either add the missing atom types to the PBSA source code and
> recompile, or settle with the inp=1 model for non-polar solvation free
> energy term.
>
> Would you like to give me some help about large difference of nonpolar
>> solvation energy and radii selection of nonpolar energy calculation? Thanks
>> in advance!
>>
>
> I didn't see any numbers, and have no idea what differences you are
> referring to. Note that inp=2 requires AmberTools to be fully patched (at
> least up to bugfix.27) in order to get the correct values for the
> dispersion energy.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 09 2013 - 19:00:03 PDT
