AMBER Archive (2009)

Subject: Re: [AMBER] ambertools for NAMD

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Thu May 07 2009 - 13:29:41 CDT

Hi all,

Thanks for your replies here is my namd configuration file

#####################################
# NAMD Configuration file for Amber #
#####################################

# set PDB and PSF file
set pdb fr.inpcrd.pdb
##set psf trimer_nr_autopsf.psf

amber on
parmfile fr.prmtop
ambercoor fr.inpcrd

set temperature 300

# Set number of minimization steps
set min 10000

# Set number of MD steps
set md 0

# Freezing atoms for minimization
set fix 1
set pme 0
set nve 0
set npt 0

#################################
# Adjustable parameters
#################################

###structure $psf
###coordinates $pdb

outputName met_water

##################################

restartfreq 500
dcdfreq 2000
xstFreq 500

outputEnergies 100
# 100 steps - every 0.2 ps
outputTiming 1000

# Shows time per step and time to completion

firsttimestep 0

#################################
# Simulation parameters
#################################

# Input
###paraTypeCharmm on

####parameters $path

temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.8333
# Cutoff is increased during minimisation
cutoff 16.
switching on
switchdist 14
# Switchdist = Cutoff - 2

# Promise that atom will not move more than 2A in a cycle
pairlistdist 18
# Cutoff + 2
stepspercycle 10
# Redo pairlists every ten steps

# Integrator Parameters
timestep 0.5
# 0.5 fs/step
rigidBonds all
# needed for 2fs steps
nonbondedFreq 1
# nonbonded forces every step
fullElectFrequency 2
# PME only every other step

###################################
#
# Temperature and Pressure control
#
###################################
###################################
#
# Constant Temperature Control
#
###################################

if {$nve==1} {
langevin on
# langevin dynamics
langevinDamping 5.
# damping coefficient of 5/ps
langevinTemp $temperature
# Random noise at this level
langevinHydrogen no
# Do not couple bath to hydrogens
}
####################################
#
#
# Pressure Control
#
#
####################################

if {$npt == 1} {
langevinPiston on
:

langevinPiston on
# Appling the langevinpiston for pressure control
langevinPistonTarget 1.01325
# One atomsheric pressure at sea level
langevinPistonPeriod 100
# barostat oscillation time scale for LP method
langevinPistonDecay 50
# barostat damping time scale for LP
LangevinPistonTemp $temperature
# barostat noise temperature for LP

# 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
}
######################################
# Fixing the protein for equilibration
# with the water
######################################
if {$fix==1} {
            fixedatoms on
            fixedatomscol B
}

# Periodic Boundary conditions

##cellBasisVector1 $x 0. 0.
# Vector next to image
##cellBasisVector2 0. $y 0.
##cellBasisVector3 0. 0. $z
##cellOrigin $x0 $y0 $z0

wrapWater on
wrapAll on
# Particle Mesh Ewald

if {$pme == 1} {
   PME yes
   PMEGridSizeX 64 ;# 3^2*2^3, close to 71.2
   PMEGridSizeY 64 ;# 2^3*3^2 , close to 71.37
   PMEGridSizeZ 64 ;# 2^7, close to 117.47
}

# the center of the cell

minimize $min
# lower potential energy for 1000 steps
reinitvels $temperature

run $md

I have now tried different versions of NAMD and it still gives the same
error message

Best

J

On Thu, May 7, 2009 at 5:16 PM, Andrew Purkiss-Trew <
a.purkiss_at_mail.cryst.bbk.ac.uk> wrote:

> It was certainly the case in older versions NAMD (2.4 and 2.5). The
> problem wasn't the actual parameters read in, but the section of the
> code that converted the Amber input files. It attempted to apply
> constraints which were not present in the Amber file (the angle terms)
> and complained about constraints that it didn't expect (the HW-HW
> term).
>
> You had to explicitly override the way it was setting up these
> constraints and it all worked. I don't know what the current state of
> play with Amber input is in NAMD, but the version that has produced the
> error is clearly not happy with the HW-HW distance and I used to have
> exactly the same symptoms.
>
> Can the original poster, e-mail his NAMD input file.
>
> On Thu, 2009-05-07 at 09:51 -0500, Wei Huang wrote:
> > For NAMD, I don't think so. It depends on how you prepare the input
> files.
> >
> > In the topology file for TIP3 water, there is a line said you need to
> have
> > H1-H2 bond if SHAKE is used.
> > "!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake"
> >
> > Jorgen, could you tell us details about how you prepare the input files?
> >
> > Cheers,
> > Wei
> >
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf
> > Of Andrew Purkiss-Trew
> > Sent: Thursday, May 07, 2009 9:30 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] ambertools for NAMD
> >
> > On Thu, 2009-05-07 at 10:09 -0400, David A. Case wrote:
> > > On Thu, May 07, 2009, Carlos Simmerling wrote:
> > >
> > > > I worry that you get a "parm file in amber 7" message- that's pretty
> > old.
> > >
> > > Believe it or not, we introduced the "new" prmtop format way back in
> Amber
> > 7.
> > > So, when VMD says "parm7", it means "parm7 or later", as opposed to the
> > "old",
> > > Amber6-and-earlier, prmtop format.
> > >
> > > > the HW-HW are likely water.
> > >
> > > I agree, and these may be treated specially in NAMD. But I'm hoping
> there
> > are
> > > NAMD users on the list who will know for sure what is going on.
> > >
> >
> > >From memory, NAMD treats TIP3P-like water differently to Amber.
> >
> > Amber uses three bonds (with Shake to constraint all the distances, 2 x
> > OW-HW and one HW-HW)
> >
> > NAMD, by default, uses the HW-OW-HW bond angle and the 2 OW-HW distances
> > to do the same thing.
> >
> > There was a way to force Amber-like behavior, but I can't remember what
> > it was off the top of my head. There should be instructions in the NAMD
> > documentation, try looking for 'use of Amber force field'
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> --
> Andrew Purkiss-Trew
> X-ray Laboratory
> London Research Institute
> Cancer Research UK
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
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>
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