From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Wed Oct 11 2006 - 18:12:54 CDT
should i use dcd file to write pdb for last frame or restart.coor file. i am
not able to write pdb from restart.coor file.
On 10/11/06, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>
> 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
>
>
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
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