From: Vishal Kopardé (vnk_sim_at_yahoo.co.uk)
Date: Wed Nov 29 2006 - 12:30:24 CST
I think you should not use "wrapNearest on" unless your simulation
box is not a rectangular parallelepiped. Are you have some unusual
geometry?
Vishal
On Nov 29, 2006, at 10:46 AM, regafan_at_usc.es wrote:
> Hello,
> I am trying to simulate a protein using NAMD, but I am having a lot
> of problems with the RATTLE error. I have looked at the NAMD-L
> archive, but it did not help. I have tried a lot of things, and at
> this moment, I don't know what to do...Please, couls somebody help me?
>
> What I did was the following:
>
> -First, from a XR protein structure, I introduced the hydrogens
> with xLeaP and minimized the whole system with AMBER (I had tried
> first introducing the hydrogens with "guesscoord" and VMD, but the
> resultant structure involved deformations related to the hydrogens
> added). I create a psf and a pdb for using with NAMD and I solvated
> and ionized this structure with the corresponding modules of VMD.
>
> -The resultant structure is minimized with NAMD in 3 steps:
> -> First, only water and ions minimization (5000 steps)
> -> Second, minimization with the backbone of the proteine
> fixed (5000 steps)
> -> Third, minimization of the whole system (10000 steps)
> The final structure has a stable energy, I show you one of the
> inputs of the minimization:
> ----------------------------------------------------------------------
> ------
> EXAMPLE MINIMIZATION
> ----------------------------------------------------------------------
> -----
> #protocol parameters
> numsteps 5000
> cutoff 9
> switching off
> binaryoutput off
> binaryrestart no
>
> #minimization parameters
> minimization on
> minTinyStep 1.0e-6
> minBabyStep 1.0e-2
> minLineGoal 1.0e-4
>
> #fixed atoms parameters
> fixedAtoms on
> fixedAtomsFile proteina_fijada.pdb
> fixedAtomsCol B
>
> # files de entrada
> structure ionized.psf
> paraTypeCharmm on
> parameters par_all22_prot.inp
> coordinates ionized.pdb
> outputname proteina_min1
> restartname proteina_min1
> exclude scaled1-4
> 1-4scaling 1.0
> ----------------------------------------------------------------------
> ----------
>
> Then, in a try to equilibrate the system, I heat it gradually
> mantaining the skeleton of the protein fixed and constraints in the
> rest of the atoms. Here you have my input file:
>
>
> ----------------------------------------------------------------------
> ----------
> INPUT FILE FOR EQUILIBRATION (1)
> ----------------------------------------------------------------------
> ----------
> rigidBonds all
> rigidTolerance 0.0005
>
> numsteps 40000
> stepspercycle 20
> firsttimestep 0
> timestep 1
> restartfreq 1000
> DCDfreq 1000
> DCDfile proteina_md1_dcd
> outputEnergies 1000
> temperature 0
> reassignFreq 1000
> reassignTemp 10
> reassignIncr 10
> reassignHold 310
>
> cutoff 10
> pairlistdist 11
> switching on
> switchdist 9
> binaryoutput no
> binaryrestart no
>
> wrapAll on
> wrapNearest on
>
> #Temperature coupling
> langevin off
> #langevinDamping 10
> #langevinTemp 310
> #langevinHydrogen no
>
> PMEGridSizeX 120
> PMEGridSizeY 180
> PMEGridSizeZ 180
> margin 5
>
> #molecular system
> structure ionized.psf
> #forcefield
> paraTypeCharmm on
> parameters par_all22_prot.inp
>
> # files de entrada
> coordinates proteina_min3.coor
> outputname proteina_md1
> restartname proteina_md1
> exclude scaled1-4
> 1-4scaling 1.0
>
> #pressure control:
> useGroupPressure yes
> useFlexibleCell yes
> useConstantRatio yes
> langevinPiston on
> langevinPistonTarget 1.01325 # in bar -> 1 atm
> langevinPistonPeriod 200
> langevinPistonDecay 200
> langevinPistonTemp 310
>
> #fixed atoms parameters
> fixedAtoms on
> fixedAtomsFile proteina_min3_backbone.pdb
> fixedAtomsCol B
>
> #constraints
> constraints on
> consref proteina_min3_99.pdb
> conskfile proteina_min3_99.pdb
> conskcol B
>
> ----------------------------------------------------------------------
> ----------
>
> After this, I turned on langevin, and decreased the constraints in
> the protein, here you have an example of one of this inputs:
>
>
> ----------------------------------------------------------------------
> ---------
> INPUT FILE FOR EQUILIBRATION (2)
> ----------------------------------------------------------------------
> ---------
>
> rigidBonds all
> rigidTolerance 0.0005
>
> numsteps 50000
> stepspercycle 20
> firsttimestep 40000
> timestep 1
> restartfreq 1000
> DCDfreq 1000
> DCDfile proteina_md2_dcd
> outputEnergies 1000
> cutoff 10
> pairlistdist 11
> switching on
> switchdist 9
> binaryoutput no
> binaryrestart no
>
> wrapAll on
> wrapNearest on
>
> #Temperature coupling
> langevin on
> langevinDamping 10
> langevinTemp 310
> langevinHydrogen no
>
> PME on
> cellOrigin 3.8 -20.6 7.6
> cellBasisVector1 90 0 0
> cellBasisVector2 0 140 0
> cellBasisVector3 0 0 125
> PMEGridSizeX 120
> PMEGridSizeY 180
> PMEGridSizeZ 180
> margin 5
> #molecular system
> structure ionized.psf
> #forcefield
> paraTypeCharmm on
> parameters par_all22_prot.inp
>
> # files de entrada
> coordinates proteina_md1.coor
> velocities proteina_md1.vel
> outputname proteina_md2
> restartname proteina_md2
> 1-4scaling 1.0
>
> #pressure control:
> useGroupPressure yes
> useFlexibleCell yes
> useConstantRatio yes
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 200
> langevinPistonTemp 310
>
> #fixed atoms parameters
> fixedAtoms on
> fixedAtomsFile proteina_md1_backbone.pdb
> fixedAtomsCol B
>
> #constraints
> constraints on
> consref proteina_md1_50.pdb
> conskfile proteina_md1_50.pdb
> conskcol B
>
> ----------------------------------------------------------------------
> ---------
>
>
> The problem appears in the next step, where the constraints in the
> protein are "25". I get error of the type:
>
> ERROR: Constraint failure in RATTLE algorithm for atom 10493!
> ERROR: Exiting prematurely.
>
>
> Changing the dimensions of the box, does not help, only changes the
> atom involved in the error. Besides, in some of the cases, I can
> see DEFORMATIONS in the residues of the protein, perhaps the source
> of the error (but why are these atoms deformed). In another cases,
> the atoms affected by the error do not present any kind of
> deformation.
>
> Please, does anybody idea of what can be happening?
>
> Thanks a lot in advance.
>
> Rebeca
> Postdoctoral student
> Parc Cientific de Barcelona
> regafan_at_usc.es
>
>
>
Send instant messages to your online friends http://uk.messenger.yahoo.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:13 CST