From: Veronika Brazdova (vb_at_chemie.hu-berlin.de)
Date: Tue Jul 31 2007 - 05:55:10 CDT
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. _________________________________________
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:01 CST