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.*
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Received on Wed Apr 10 2024 - 21:30:02 PDT
