From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Oct 11 2006 - 15:04:10 CDT
consref can only take a pdb as input, not a binary coordinate file.
Use VMD to load the coordinates and then write a pdb containing them.
On Oct 11, 2006, at 2:28 PM, Dhiraj Srivastava wrote:
> Hi all
> I am trying to restrain my protein and equilibrate the
> system. when i am trying to restart my simulation, then i am
> getting error message like
>
> charm++ fetal error
> FATAL ERROR : Line too long in pdb file min/prodh_wb_min.restart.coor
>
> but when i am setting my restrain off then i am able to restart the
> simulation. my config file looks like.
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # Ubiquitin in a Water Sphere
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../common/prodh_wb.psf
> coordinates ../common/prodh_wb.pdb
>
> set temperature 100
> set outputname equil100/prodh_wb_min
>
> if {1} {
> set inputname min/prodh_wb_min
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the
> "temperature" entry if you use this!
> extendedSystem $inputname.xsc
> }
>
> firsttimestep 10000
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_lipid.inp
> #temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Periodic Boundary Conditions
> cellBasisVector1 -81.875 0.0 0.0
> cellBasisVector2 0.0 -79.3840036392 0.0
> cellBasisVector3 0.0 0.0 -81.5929965973
> cellOrigin 5.72501993179 45.225315094 49.4890518188
>
> #wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 82
> PMEGridSizeY 80
> PMEGridSizeZ 82
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> #les off
> #lesFactor 10
> #lesReduceTemp on
> #lesReduceMass on
> #lesCol B
>
> constraints on
> consexp 2
> consref $inputname.restart.coor
> conskfile ../common/prodh_wb_res5.pdb
> conskcol B
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> #minimize 10000
> #reinitvels $temperature
> run 10000 ;# 600ps
>
>
> i am not understanding the problem as i am following the manual. is
> there any problem in my way of defining consref file name. i am
> taking coordinates for this file from previous simulation.
>
>
>
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
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