From: Brian Radak (bradak_at_anl.gov)
Date: Mon Jul 17 2017 - 15:55:21 CDT
Hi Marawan,
Unfortunately, I don't believe alchemical calculations are currently
compatible with AMBER format.
Brian
On 07/17/2017 11:45 AM, Marawan Hussien wrote:
> 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.top
> ambercoor eq_5_npt.rst7
>
>
> bincoordinates com_2.restart.coor
> binVelocities com_2.restart.vel
> extendedsystem 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.vel
> restartfreq 1000; # 500 steps = every 1ps
> dcdfreq 1000;
>
>
> xstFreq 1000; # XSTFreq: control how often the extended
> systen configuration
> # will be appended to the XST file
> outputEnergies 1000; # 125 steps = every 0.25ps
> # The number of timesteps between each energy
> output of NAMD
> outputTiming 1000; # The number of timesteps between
> each timing output shows
> # time per step and time to completion
>
> # Force-Field Parameters
> amber on
> useSettle 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 on
> watermodel tip3
>
> stepspercycle 20; # 20 redo pairlists every ten steps
> pairlistsPerCycle 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 Parameters
> timestep 2.0; # fs/step
> rigidBonds all; # Bound constraint all bonds
> involving H are fixed in length
> nonbondedFreq 1; # nonbonded forces every step
> fullElectFrequency 1; # PME every step
>
>
>
>
> wrapWater on; # wrap water to central cell
> wrapAll on; # wrap other molecules too
>
> # PME (for full-system periodic electrostatics)
> PME yes;
> PMEGridSpacing 1;
> margin 6
>
> # Pressure and volume control
> useGroupPressure yes; # use a hydrogen-group based
> pseudo-molecular viral to calcualte pressure and
> # has less fluctuation, is needed for rigid bonds
> (rigidBonds/SHAKE)
>
>
> langevin on
> langevinDamping 1
>
> langevinHydrogen off
>
> # constant pressure
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 50.0
> langevinPistonDecay 25.0
> langevinTemp 310
> langevinPistonTemp 300
>
>
>
> minimize 500
> run 1000
>
> source fep.tcl
> #
> alch on
> alchFile bound.fep
> alchCol B
> alchOutFreq 10
> alchOutFile system.fepout
> alchEquilSteps 500
> #
> set nSteps 2000
> #
>
> runFEP 0.0 1.0 0.1 $numSteps
> #####
>
> Whenever I run the file, I got this error:
>
> #####
> FINISHED WRITING RESTART VELOCITIES
> The last velocity output (seq=1000) takes 0.014 seconds, 202.688 MB of
> memory in use
> Info: Benchmark time: 1024 CPUs 0.0103227 s/step 0.0597378 days/ns
> 202.688 MB memory
> TCL: Setting parameter alch to on
> FATAL 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
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:26 CST