Dear Dr. Jason Swails and Miguel Ortiz Lombardía,
thank you very much for your useful help.
Regarding the Mg2+ ions:
as suggested, I will search in the literature if there is any particular prescription.
Regarding the nonlinear PB calculation:
I run the calculations following the last Miguel's suggestions.
However, it seems that an other error is present in the calculations.
Indeed, I had the following error:
Beginning PB calculations with /softmp/AMBER12/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /softmp/AMBER12/amber12/bin/mmpbsa_py_energy failed with prmtop TOPO2_DNA_F14.prmtop!
PB Bomb in pb_read(): cutnb=0 cannot be used with eneopt=1 0.0000000000000000 1
>From the amber12-manual, I read that
when eneopt=1 (as in my case), cutnb is the cutoff distance used for van der Waals interactions only.
Moreover, eneopt=1 requires a non-zero CUTNB and BCOPT = 5.
Now, I am running a test calulation with cutnb=1 (to see if I reach any reasonable result)
However, in the manual,there is not specified value for cutnb when eneopt=1.
In your experience, do you have any suggestion about the value of cutnb when eneopt=1 ??
Thank you very much
giulia
________________________________________
Da: Jason Swails [jason.swails.gmail.com]
Inviato: giovedì 21 marzo 2013 23.37
A: AMBER Mailing List
Oggetto: Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions
On Thu, Mar 21, 2013 at 11:52 AM, Miguel Ortiz Lombardía <
miguel.ortiz-lombardia.afmb.univ-mrs.fr> wrote:
>
> Hi Jason,
>
> Well, I did not answer to the Mg2+ question ;-)
>
> As for NAB not dealing with non-linear PB, I may be wrong, it may be
> incompatible with some other option... I carried out many tests and
> somehow this is what I remember. But I cannot track down now why I think
> NAB does not deal with non-linear PB, sorry.
>
Ah, I guess I read too quickly. Well then in response to the Mg2+ question
from the OP, there is no prescription for dealing with explicit ions in PB
or GB solvents. You can try running the calculations including whatever
ions you want to include, but check the results carefully to make sure they
make sense.
I would also encourage searching the literature for researchers that tried
something similar to see how they approached the issue.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 22 2013 - 02:30:03 PDT
