[gmx-users] Gromacs multisubunit defragmentation

[Muhammad Hagras]

Thanks Justin for your help,

I am also surprised from that subunit movements!

Here are the commands that I used in sequence:

1- pdb2gmx_d -f protein.pdb -o protein.gro -p protein.top
2- editconf_d -f protein.gro -o protein_pbc.gro -d 1.0
3- grompp_d -v -f minim.mdp -c protein_pbc.gro -p protein.top -o protein.tpr
4- mdrun_d -v -deffnm protein -c protein_EM.pdb

Thanks for help,

Muhammad

On Tue, Jun 14, 2016 at 4:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/13/16 9:26 PM, Muhammad Hagras wrote:
>
>> Hi folks,
>>
>> I need some help in running EM on three subunits protein (not covalently
>> bonded),
>>
>> When I run EM on such molecule in vacuum or in implicit solvent, the three
>> subunits move apart ?! I tried with and without pbc and with and without
>> implicit solvent and still the same results!
>>
>>
> That seems somewhat impossible.  Without PBC, there is no box and
> therefore atoms/molecules don't jump.  You're applying restraints, so there
> shouldn't be any really large movement.  "Broken" molecules are due to PBC,
> so all you're seeing is the fact that with PBC, you haven't set up the box
> appropriately.  But you haven't provided enough information (all commands
> up to this point, including how you set up the box), so it's a bit of a
> guess.
>
> -Justin
>
>
>
>> Here is my minim.mdp I used
>> -------------------------------------------------------------------
>> title           = Energy Minimization   ; Title of run
>>
>> ; The following line tell the program the standard locations where to find
>> certain files
>> cpp             = /lib/cpp      ; Preprocessor
>>
>> ; Define can be used to control processes
>> define          = -DPOSRES
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator      = cg            ; Algorithm (steep = steepest descent
>> minimization)
>> emtol           = 10.0          ; Stop minimization when the maximum force
>> < 1.0 kJ/mol
>> nstcalclr       = 1
>> nstcgsteep      = 10000
>> dt              = 0.001
>> nsteps          = 1000000000            ; Maximum number of (minimization)
>> steps to perform
>> nstenergy       = 10000         ; Write energies to disk every nstenergy
>> steps
>> energygrps      = System        ; Which energy group(s) to write to disk
>> ;freezegrps     = Backbone
>> ;freezedim      = Y Y Y
>> rlist           = 1.0
>> lincs_order     = 8
>> lincs_iter      = 4
>> nstcomm         = 1
>> nstcalcenergy   = 1
>> cutoff-scheme = group
>>
>> comm_mode       = Linear
>> ;nstcomm        = 1
>> ;dispcorr       = EnerPres
>> ;optimize_fft   = yes
>> ;pme_order      = 6
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> ns_type         = grid;simple   ; Method to determine neighbor list
>> (simple, grid)
>> coulombtype     = PME;cut-off   ; Treatment of long range electrostatic
>> interactions
>> vdwtype         = cut-off
>> rcoulomb        = 1.0           ; long range electrostatic cut-off
>> rvdw            = 1.0   ; long range Van der Waals cut-off
>> ;constraints    = all-bonds             ; Bond types to replace by
>> constraints
>> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)i
>>
>>
>> ; IMPLICIT SOLVENT ALGORITHM
>> implicit_solvent         = no;gbsa
>>
>> ; GENERALIZED BORN ELECTROSTATICS
>> ; Algorithm for calculating Born radii
>> gb_algorithm             = Still;OBC
>> ; Frequency of calculating the Born radii inside rlist
>> nstgbradii               = 1
>> ; Cutoff for Born radii calculation; the contribution from atoms
>> ; between rlist and rgbradii is updated every nstlist steps
>> rgbradii                 = 1.0
>> ; Dielectric coefficient of the implicit solvent
>> gb_epsilon_solvent       = 4
>> ; Salt concentration in M for Generalized Born models
>> gb_saltconc              = 0
>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>> gb_obc_alpha             = 1
>> gb_obc_beta              = 0.8
>> gb_obc_gamma             = 4.85
>> gb_dielectric_offset     = 0.009
>> sa_algorithm             = Ace-approximation
>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>> sa_surface_tension       = 2.25936
>>
>> -----------------------------------------------------------------------
>>
>> Thanks for help,
>>
>> Muhammad Hagras
>> PhD, Biophysics UCD
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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