AW: problems running amber parm7

From: Norman Geist (
Date: Tue Jan 20 2015 - 01:38:30 CST


Von: Francesco Pietra []
Gesendet: Dienstag, 20. Januar 2015 08:25
An: NAMD; Norman Geist
Betreff: Re: namd-l: problems running amber parm7


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.


I mean that the FF has changed.



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?).

Fixed atoms or positional harmonic constraints, see manual.

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.

Are you sure? VMD must show all bonds if they are written in the parmfile. I’m using amber aswell and do not have such issues. The naming issue is mostly only an alignment problem. Where VMD/NAMD align 3 character names like “ H12” amber expects “H12 ”. If you have messages about “added missing atoms” when loading a pdb to leap which produces duplicates, you have likely an issue with the name alignment. An easy option can be to just strip out all the hydrogens and other critical atoms. I have scripts that repair that stuff for me, so if I load a pdb to xleap, I get no complaining at all.

You can send me the pdb and I’ll check it for format issues.

Norman Geist




On Tue, Jan 20, 2015 at 7:19 AM, Norman Geist <> wrote:


Von: [] Im Auftrag von Francesco Pietra
Gesendet: Montag, 19. Januar 2015 20:04
Betreff: namd-l: problems running amber parm7






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. It 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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