Re: vdW parameter for atom type CN7 in ATP

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jul 31 2007 - 06:18:24 CDT

Hi Veronika,

This should solve your problem: change the parameter file
"par_all27_prot_lipid.inp" for "par_all27_prot_na.inp" in your input
file.

Maj sa,

Michel

2007/7/31, Veronika Brazdova <vb_at_chemie.hu-berlin.de>:
> Dear all,
>
> I have a protein with an ATP molecule. A NAMD simulation crashes with
> the following error message:
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CN7
>
> It is not the problem discussed some time ago on this list, where CN7 in
> ATOM C2' CN7 0.14 and ATOM C5' CN8 -0.08 had to be changed to CN7B,
> because the toppar_all27_na_nad_ppi.str file I am using already has
> these atoms corrected to CN7B. In any case, even if I change the
> remaining two CN7 atoms to CN7B and repeat the whole psf-creation
> procedure I get the same error message from NAMD, only it then reads
> ... ATOM TYPE CN7B.
>
> The only CN7 type atoms in the system are in the ATP molecule.
>
> Here are more details: I created a .psf file using
>
> package require psfgen
> topology top_all27_na.rtf
> topology toppar_all27_na_nad_ppi.str
> topology top_all27_prot_lipid.inp
> segment B { pdb chainB_top.pdb }
> coordpdb chainB_top.pdb B
> guesscoord
> #and the same for other chains
> writepsf combined.psf
> writepsf combined.pdb
>
> I am using the toppar_c32b1.tar.gz topology and parameter files.
>
> My NAMD config file is as follows:
> structure combine.psf
> coordinates combine.pdb
> set temperature 310 ;
> temperature $temperature ;# initialize velocities randomly
> numsteps 50000 ;# run stops when this step is reached
> outputName combine_out;# base name for output from this run
> restartfreq 500 ;# 500 steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100 ;# 100 steps = every 0.2 ps
> outputTiming 1000 ;# shows time per step and time to completion
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> parameters toppar_all27_na_nad_ppi.str
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> cutoff 12. ;# may use smaller, maybe 10., with PME
> switchdist 10. ;# cutoff - 2.
> pairlistdist 14. ;# cutoff + 2.
> stepspercycle 10 ;# redo pairlists every ten steps
> timestep 1.0 ;# 2fs/step
> rigidBonds water ;# needed for 2fs steps
> nonbondedFreq 1 ;# nonbonded forces every step
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> cutoff 12. ;# may use smaller, maybe 10., with PME
> switchdist 10. ;# cutoff - 2.
> pairlistdist 14. ;# cutoff + 2.
> stepspercycle 10 ;# redo pairlists every ten steps
> timestep 1.0 ;# 2fs/step
> rigidBonds water ;# needed for 2fs steps
> nonbondedFreq 1 ;# nonbonded forces every step
> fullElectFrequency 2 ;# PME only every other step
> # Constant Temperature Control
> langevin on ;# langevin dynamics
> langevinDamping 5. ;# damping coefficient of 5/ps
> langevinTemp $temperature ;# random noise at this level
> langevinHydrogen no ;# don't couple bath to hydrogens
>
> # Periodic Boundary conditions
> cellBasisVector1 28.0 0. 0. ;# vector to the next image
> cellBasisVector2 0. 28.0 0.
> cellBasisVector3 0. 0 35.0
> cellOrigin 0. 0. 0. ;# the *center* of the cell
>
> # Wrapping ounly affects output, not the simulation
> wrapWater on ;# wrap water to central cell
> wrapAll on ;# wrap other molecules too
> wrapNearest off ;# use for non-rectangular cells
>
> # Particle mesh Ewald
> # (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 32 ;# 2^5, close to 31.2
> PMEGridSizeY 45 ;# 3^2 * 5, close to 44.8
> PMEGridSizeZ 54 ;# 2 * 3^3, close to 51.3
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigid bonds
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, maybe for membrane
>
> #fixedAtoms on
> #fixedAtomsFile myfixedatoms.pdb ;# flags are in this file
> #fixedAtomsCol B ;# set beta non-zero to fix an atom
>
> # Here the commands start
> minimize 1000 ;# lower potential energy for 1000 steps
> reinitvels $temperature ;# since minimization zeros velocities
> run 50000 ;# 100ps
>
> Thanks for help!
>
> Veronika
>
> --
> _________________________________________
>
> Veronika Brazdova
> Department of Physics & Astronomy
> University College London
> Gower Street
> WC1E 6BT, London, U.K.
> _________________________________________
>

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