From: Marawan Hussien (marawanhussain_at_yahoo.com)
Date: Mon Jul 17 2017 - 11:45:22 CDT
Hi,I am having trouble running absolute binding free energy calculation for a solvated protein ligand complex built with AMBER.Here is my NAMD configuration file:
######parmfile com_solvated.topambercoor eq_5_npt.rst7
bincoordinates com_2.restart.coorbinVelocities com_2.restart.velextendedsystem com_2.restart.xsc
set temperature 300;
set outputname com_4;
outputName $outputname; # base name for output from this run # NAMD writes two files at the end, final coord and vel # in the format of first-dyn.coor and first-dyn.velrestartfreq 1000; # 500 steps = every 1psdcdfreq 1000;
xstFreq 1000; # XSTFreq: control how often the extended systen configuration # will be appended to the XST fileoutputEnergies 1000; # 125 steps = every 0.25ps # The number of timesteps between each energy output of NAMDoutputTiming 1000; # The number of timesteps between each timing output shows # time per step and time to completion
# Force-Field Parametersamber onuseSettle on rigidTolerance 1.0e-8 cutoff 13.5 pairlistdist 16.0 switching off exclude scaled1-4 readexclusions yes 1-4scaling 0.83333333 scnb 2.0 zeromomentum on ljcorrection onwatermodel tip3
stepspercycle 20; # 20 redo pairlists every ten stepspairlistsPerCycle 2; # 2 is the default # cycle represents the number of steps between atom reassignments # this means every 20/2=10 steps the pairlist will be updated # Integrator Parameterstimestep 2.0; # fs/steprigidBonds all; # Bound constraint all bonds involving H are fixed in lengthnonbondedFreq 1; # nonbonded forces every stepfullElectFrequency 1; # PME every step
wrapWater on; # wrap water to central cellwrapAll on; # wrap other molecules too
# PME (for full-system periodic electrostatics)PME yes;PMEGridSpacing 1;margin 6
# Pressure and volume controluseGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and # has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)
langevin onlangevinDamping 1
langevinHydrogen off
# constant pressurelangevinPiston onlangevinPistonTarget 1.01325langevinPistonPeriod 50.0langevinPistonDecay 25.0langevinTemp 310langevinPistonTemp 300
minimize 500run 1000
source fep.tcl#alch onalchFile bound.fepalchCol BalchOutFreq 10alchOutFile system.fepoutalchEquilSteps 500#set nSteps 2000#
runFEP 0.0 1.0 0.1 $numSteps #####
Whenever I run the file, I got this error:
#####FINISHED WRITING RESTART VELOCITIESThe last velocity output (seq=1000) takes 0.014 seconds, 202.688 MB of memory in useInfo: Benchmark time: 1024 CPUs 0.0103227 s/step 0.0597378 days/ns 202.688 MB memoryTCL: Setting parameter alch to onFATAL ERROR: Setting parameter alch from script failed!FATAL ERROR: Setting parameter alch from script failed!#####
Nothing helped, I tried some suggestions, such as including this keyword:global at k r0
Or adding explicit parameters for softcore potentials, but in vain. I also tried to use the same input while imposing constrains on the ligand (5 kcal/mol) cartesian constrains, but this also did not help. I am not sure if there is any incompatibility between the tcl forces from the configuraion file and the fep.tcl script. Any suggestion?
Regards,Marawan
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