Zoran,
to the best of my knowledge, all ions are stripped off the structures
prior to MMPBSA treatment, normally. (There might be, however, special
cases, where ions are considered part of the ligand or receptor.)
Since the 'postproduction' MMPBSA analysis is not performed with
periodic boundary conditions but using a continuum solvent apporach (PB
or GB), a total charge different from 0 is not an algorithmic problem.
Maybe this helps.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 10/28/2021 03:57 PM,
zmatovic.kg.ac.rs wrote:
> Dear Amber friends,
>
> I used again to check my perception about deltaG determination across MMPBSA
> (tutorial http://ambermd.org/tutorials/advanced/tutorial3). Namely, some
> inconsistency appear between ras_raf and estrogen_raloxifen cases. In the
> first case (using both ways mm_pbsa.pl and MMPBSA.py) the total system
> ras_raf is neutral so there is no need for adding counterions after
> solvations (both methods). However, in case of estrogen_raloxifen
> (https://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.php)
> solvated 1err.solvated.prmtop parameter file charge the unit with -7 so as
> the complex.prmtop and receptor.prmtop files. So I wonder is this
> postprocessing (after production) treatment or something else..? Does it
> mean we shouldn't have any ion within solvated, complex_dry, receptor and
> ligand files? May be this is already explained in some already posted quests
> in this group and if so I am excusing myself and ask kindly to direct me to
> that post.
>
>
>
> I wish you all to have a very nice day.
>
> Zoran
>
>
>
>
>
>
>
>
>
>
>
> A true friend is someone who is there for you
>
> when he'd rather be anywhere else.
>
> -- Len Wein
>
>
>
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Received on Thu Oct 28 2021 - 08:30:03 PDT
