Minimization with NAMD

From: valesrdp (
Date: Mon May 09 2005 - 09:17:57 CDT


I'm studying a protein and I'm following this procedure: minimization of the
protein, MD simulation and minimization of some frames from my MD.
With regard to the minimization after the MD, I didn't find a way to set the
value of the gradient convergence but I check the value of the “Gradient
Tolerance” to be lower than 5. Do you think my procedure is correct?
Moreover, when I minimize the frames from MD, I always observe a problem with
hydrogen atom bound to the indolic nitrogen of TRP residues: this hydrogen is
never coplanar with respect to the whole residue.
I used the script which is pasted below. I tried more than once, modifying
different parameters, but I always got the same problem.

Can you suggest me how to modify my file .conf?

Thank you in advance for any help,


# My file .conf

# initial config
coordinates my.pdb
temperature 0

# output params
outputname my_eq
binaryoutput off

# force field params
paraTypeCharmm on
structure my.psf
parameters par_all27_prot_lipid.inp
exclude 1-2 (I tried to use scaled1-4 but I got worst results)
#1-4scaling 1.0
switching on
switchdist 5.0
cutoff 8.0
pairlistdist 14.0
margin 0.1

#Integrator parameter
#timestep 2.0 ;# 2fs/step
#rigidBonds all ;# needed for 2fs steps
#nonbondedFreq 1
#fullElectFrequency 2
#stepspercycle 10

# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 10.6278522891, -18.6494389115, 26.0904352648
sphericalBCr1 60.0
sphericalBCk1 10
sphericalBCexp1 2

minimize 50000

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