From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jan 20 2015 - 01:25:17 CST
>
> you have changed your parameters to parm10,
>
Perhaps I was unclear. I wrote that now, with parm10, I am using the same
min.conf settings used before with parm9. However, present system was built
from scratch by using ambertools14, i.e., parm10.
If definitely everything is ok with your system, than you’d like to put
> some hbond restraints (extrabonds) to your minimization (and maybe
> equilibration) to prevent the protein from unfolding.
>
As I had no problems by using GBIS-SASA, I'll try now by removing all
crystallization water in setting up the system in periodic boxes.
May I ask how to restrain the whole protein - to let water equilibrating -
in this context (fixing atoms, colvars?).
The lack of segnames, particularly for crystal water and the different
chains, and the renumbering of residues in amber life uneasy. In addition
to (1) amber adpting pdb and namd xplor atom names (2) vmd not showing all
chemical bonds commanded on leap and which are written in .parm7 files. So,
I am faced with the difficulty of combining the amber withe xplor worlds.
Sometimes uneasy.
thanks
francesco
On Tue, Jan 20, 2015 at 7:19 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Francesco Pietra
> *Gesendet:* Montag, 19. Januar 2015 20:04
> *An:* NAMD
> *Betreff:* namd-l: problems running amber parm7
>
>
>
> Hello:
>
>
>
> Hey
>
>
>
> I am experiencing problems in running amber parm7/rst (parm10) in periodic
> box tip3p solvation. I used the same settings that proved efficient in past
> work with parm9 for a protein with a metallic center:
>
>
>
>
>
> # Approximations for nonbonded interactions
>
> cutoff 9 # for vdW and elctrostatic interactions
>
> switching on
>
> switchDist 6 # < cutoff
>
> pairListDist 11 # between pair of atoms for vdW and electrost
>
> outputpairlists 1000
>
> margin 0
>
>
>
> These settings are unusual, defaults are:
>
>
>
> cutoff 10
>
> switchdist 9 #cutoff -1
>
> pairlistdist 12 #cutoff+2
>
>
>
> # Multistep integrator parameters
>
> timestep 1.5 # 1.5 fs/step
>
> nonbondedFreq 2 # nonbonded forces every two steps
>
> stepspercycle 20 # redo pairlist every 20 steps
>
> fullelectfrequency 2 # number of timesteps between electr evaluation
>
>
>
> A timestep of 2fs would be possible when using rigidbonds all.
>
>
>
> # PME settings
>
> PME on
>
> PMETolerance 1.0e-6
>
> PMEInterpOrder 4 # i.e. cubic spline
>
> PMEGridSizeX 147 # size of fftw grid on x dimension
>
> PMEGridSizeY 115
>
> PMEGridSizeZ 102
>
> PMEGridSpacing 1.0
>
>
>
> Settings PMEGridSpacing and PMEGridSize* is redundant.
>
>
>
> # periodic settings
>
> # Don't set the periodic cell basis if you have also specified an .xsc
>
> # cellBasisVector1 138.96 0. 0.
>
> # cellBasisVector2 0. 105.38 0.
>
> # cellBasisVector3 0. 0. 91.97
>
> cellOrigin 71.08314514160156 54.25843811035156 47.91973114013672
>
>
>
> # output
>
> outputName ./min-05
>
> outputEnergies 500 ;# multiple of fullElectFrequency or viceversa
>
> restartfreq 100
>
> binaryrestart yes
>
> binaryoutput no
>
> # wrapNearest no
>
> # wrapAll on
>
>
>
> Your restart freq is way too low. You are writing a restart every approx.
> minute.
>
>
>
> seed 3971
>
>
>
> Why you set the seed manually?
>
>
>
> # Minimize protocol (steps multiple of stepspercycle)
>
> # minimization on # default off
>
> minTinyStep 1.0e-6 # default 1.0e-6
>
> minBabyStep 1.0e-2 # default 1.0e-2
>
> minLineGoal 1.0e-4 # default 1.0e-4
>
>
>
> Why pumping up the script with so much values that are set to default
> anyway?
>
>
>
> velocityQuenching on # default off
>
> maximumMove 1.5 # default 0.75 x cutoff/stepsPerCycle = 0.5
>
>
>
>
>
> Minimization proved difficult so that I went to velocityQuenching. That
> went on well from ts/VelQuen 0.01/0.01 to 1.5/1.5, the last for 1000 steps.
> Continuing under the latter conditions caused notable denaturation of the
> protein (loss of alpha helicitiy) while the water box, from cubic became
> nearly spherical.
>
>
>
> Now to you actual problem. Away from the comments above, especially cutoff
> and switchdist, you have changed your parameters to parm10, so it’s not
> unlikely that your molecule behave slightly different (have you checked
> what changes have been made by the amber folks). But given the fact that
> you were not able to simply minimize your system, I’d suspect that
> something is wrong with your initial input (close contacts etc.). What
> exactly prevents you from doing a standard minimization (error message)? If
> definitely everything is ok with your system, than you’d like to put some
> hbond restraints (extrabonds) to your minimization (and maybe
> equilibration) to prevent the protein from unfolding.
>
>
>
> The enzyme comprises several chains and a transition-metal active center,
> bound to the protein backbone through covalent carbon-carbon bonds. The
> conformation of the active center is maintained well until min-05 as the
> protein above, then it suffers somewhat from the protein degradration.
>
>
>
> I wonder whether more appropriate settings could be used. I*t is
> important to mention that no denaturation of the protein was observed under
> implicit conditions (GBIS/SASA) even on heating to 300K.*
>
>
>
> Thanks for advice
>
> francesco pietra
>
>
>
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