[gmx-users] Gromacs multisubunit defragmentation

[Justin Lemkul]

On 6/14/16 12:45 PM, Muhammad Hagras wrote:
> 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
>

I don't see how this sequence would lead to any issues, with or without PBC. 
But in any case, for visualization purposes, just re-image using trjconv.

-Justin

> 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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-- 
==================================================

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

==================================================