Hello Amber Users,
I am attempting to use Paramfit to generate parameters for molecules of interest. In my initial trial I was able to run paramfit from start to finish with 20 structures. I wanted to repeat the process but this time with about 350 structures. This time I can only complete the first step to fit K with that many structures. After that I use the following job control file.
# Run a fit to energies using the parameters defined earlier
RUNTYPE=FIT
COORDINATE_FORMAT=TRAJECTORY
NSTRUCTURES=364
K=-292501548281.682251
PARAMETERS_TO_FIT=LOAD
PARAMETER_FILE_NAME=prms.in
FUNC_TO_FIT=SUM_SQUARES_AMBER_STANDARD
QM_ENERGY_UNITS=HARTREE
# Use the genetic algorithm with the following settings
ALGORITHM=GENETIC
OPTIMIZATIONS=50
MAX_GENERATIONS=10000
GENERATIONS_TO_CONV=20
GENERATIONS_TO_SIMPLEX=5
GENERATIONS_WITHOUT_SIMPLEX=5
MUTATION_RATE=0.100000
PARENT_PERCENT=0.250000
SEARCH_SPACE=-1.000000
SORT_MDCRDS=OFF
# Output files for later analysis
WRITE_ENERGY=fit_output_energy.dat
Every time I run it says “Killed” after about 30-40 minutes. Additionally it throws these errors.
-bash-4.2$ -350.1297 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
bash: -350.1297: command not found...
-bash-4.2$ (n -c3-nh-ce)*Kp = 351.1492 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (n -c3-nh-c3)*Kp = -23.1425 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (n -c -c3-nh)*Kp = 93.5440 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (n -c -c3-c3)*Kp = -73.0671 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (n -c -c3-c3)*Kp = 23.1595 kcal/mol, Np = 4.0000, Phase = 180.0001 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (nh-ce-ce-c2)*Kp = -219.8412 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (nh-c3-n -c3)*Kp = 146.5671 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (nh-c3-n -c )*Kp = 60.3180 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (nh-c3-c -o )*Kp = -14.6946 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (nh-c3-c3-ca)*Kp = 896.3533 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (c3-c3-nh-ce)*Kp = 843.2682 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (c3-c3-n -c3)*Kp = -24.0452 kcal/mol, Np = 2.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (c3-c3-n -c )*Kp = 77.9657 kcal/mol, Np = 1.0000, Phase = 180.0001 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (c3-c3-n -c )*Kp = 28.4979 kcal/mol, Np = 3.0000, Phase = 0.0000 Deg
-bash: syntax error near unexpected token `*Kp'
-bash-4.2$ (c3-c3-n -c )*Kp = 32.4247 kcal/mol, Np = 4.
-bash: syntax error near unexpected token `*Kp’
The parameters that I’m setting to fit about 64 dihedral angles using the KP setting.
Has anyone encountered a problem similar to this? Is it that I am simply using too many structures, or is there a different problem? If the problem has to do with the amount of structures how many structures are usually necessary to create good parameters?
Thanks in advance for the help.
-Sam
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Received on Fri Aug 14 2020 - 15:00:02 PDT
