VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Aug 12 2006 - 12:02:28 CDT

The angle still essentially doesn't exist since that inserted line gives it
a force constant of zero.

Try this (obviously, k = 50 is just a guess, based on all other k-thetas):

HT HT OT 50.0 127.74

Hopefully with this you will have a simulation that runs at least.

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
sseefeld_at_uwm.edu
Sent: Saturday, August 12, 2006 11:51 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: NAMD minimization error

I modified my wild type cytochrome c by putting the TML at position 72 and
solvating the protein with a water box using this script.

package require psfgen

topology top_all27_prot_lipid_ycc.inp

pdbalias residue HEM HEME

pdbalias residue HOH TIP3

segment B {pdb 2YCC.pdb

mutate 72 TML}

coordpdb 2YCC.pdb B

guesscoord

writepdb 2YCCtml.pdb

writepsf 2YCCtml.psf

package require solvate

solvate 2YCCtml.psf 2YCCtml.pdb -t 7 -o 2YCCtml_wb

The min max came out as
{-21.3059997559 -6.99700021744 -20.3220005035} {29.9920005798 44.0239982605
32.9550018311}

meaning the center is approx
4.343 18.5135 6.3165

using this i setup my namd minimization

# input
structure 2YCCtml_wb.psf
coordinates 2YCCtml_wb.pdb
paraTypeCharmm on
parameters par_all27_prot_lipid_ycc.inp

numsteps 100
minimization on

# force field parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching On
switchdist 12.0
pairlistdist 16.0

# integrator params
timestep 1.0
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Periodic boundary condition
cellBasisVector1 48 0 0
cellBasisVector2 0 48 0
cellBasisVector3 0 0 48
cellorigin 4.3 18.5 6.3
wrapWater on
wrapAll on
wrapNearest on

# output
outputname 2YCCtml_wb_min.pdb
dcdfile 2YCCtml_wb_min.dcd

binaryoutput no
outputEnergies 100
dcdfreq 100

This gives me the

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT

I looked on the mailing list and I couldn't find a solution for that other
than
using a diffent program. So I decided to find a parameter file that did have
this bond specified because I was not interested in the validity of my data
just yet but more in seeing if I could get this to running at the moment.

I grabbed this line from
http://www.cs.washington.edu/homes/tapan/projects/GBP/figures/PARM.PRM which
i
simply found using a google search.
HT HT OT 0.0 127.74

When I now run the simulation with this new parameter file I get my terminal
screen entirely filled with

INITIAL STEP: 1e-300
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
NEW SEARCH DIRECTION

Over and over again so fast that I cannot see anything that happens before
it.
Any help in resolving this issue to help me keep moving forward would be
greatly appreciated.

Thanks in advance,
Sean Seefeld