Why are you trying to find a reference energy for a residue INSIDE the
protein ???
That is NOT what that script is for.
in constant pH runs you find the reference energy for tyrosine in the
model peptide (which by the way, it has already been done for you,
unless you are using a force field combination different than the one
already parametrized in amber for constant pH), and then just run
constant pH MD for the protein.
You NEVER calculate a reference energy for the residue inside the protein.
Adrian
On 4/11/24 12:29 AM, Dulal Mondal via AMBER wrote:
> [External Email]
>
> Dear Experts,
>
> *I calculate the reference energy of model tyrosine (ACE-TYR-NME) using the
> following command*:.
>
> finddgref.py -mdexec $exe -i cp_ph7.in -o prod1.out -p
> ../min/TYR_model.prmtop -c ../nvt/nvtequi.ncrst -r prod1.ncrst -x prod1.nc
> -cpin TYR.cpin -cpout prod1.cpout -cprestrt prod1.cpin
>
> *After completion of run, it shows the following output message:*
>
> AMBER execution #10: running 1000000 MD steps of equilibration for
> DELTAGREF = -65.060731 kcal/mol
> AMBER execution #10: running 10000000 MD steps of production for
> DELTAGREF = -65.060731 kcal/mol
> The fraction of protonated species is 53.60% for the Residue 'TYR 2'
> AMBER execution #11: running 1000000 MD steps of equilibration for
> DELTAGREF = -64.974735 kcal/mol
> AMBER execution #11: running 10000000 MD steps of production for
> DELTAGREF = -64.974735 kcal/mol
> The fraction of protonated species is 52.40% for the Residue 'TYR 2'
> AMBER execution #12: running 1000000 MD steps of equilibration for
> DELTAGREF = -64.917460 kcal/mol
> AMBER execution #12: running 10000000 MD steps of production for
> DELTAGREF = -64.917460 kcal/mol
> The fraction of protonated species is 50.10% for the Residue 'TYR 2'
>
> *The value of DELTAGREF that gives a converged fraction of protonated
> species for 10000000 MD steps and for solvent pH = 9.600 equals to 50.10%
> is: DELTAGREF = -64.917460 kcal/mol*
> * The execution of finddgref.py ended with success.*
>
> *But when I performed the same task for TYR 5 in protein, i got an error
> message.*
>
> AMBER execution #10: running 1000000 MD steps of equilibration for
> DELTAGREF = -51.998153 kcal/mol
> AMBER execution #10: running 10000000 MD steps of production for
> DELTAGREF = -51.998153 kcal/mol
> The fraction of protonated species is 0.10% for the Residue 'TYR 5'
> AMBER execution #11: running 1000000 MD steps of equilibration for
> DELTAGREF = -56.115669 kcal/mol
> AMBER execution #11: running 10000000 MD steps of production for
> DELTAGREF = -56.115669 kcal/mol
> The fraction of protonated species is 100.00% for the Residue 'TYR 5'
> Traceback (most recent call last):
> File "/home/srabani/Downloads/amber18/bin/finddgref.py", line 1311, in
> <module>
> main(opt)
> File "/home/srabani/Downloads/amber18/bin/finddgref.py", line 1231, in
> main
> EstimateDG(opt,log,data)
> * File "/home/srabani/Downloads/amber18/bin/finddgref.py", line 597, in
> EstimateDG*
> * data.dg += data.KB*data.temp0*data.factor*math.log(1.0/data.frac-1.0)*
> *ValueError: math domain error*
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Apr 11 2024 - 08:00:02 PDT
