[gmx-users] Issue in Energy minimization protein-ligand complex

[Sainitin Donakonda]

Hi Justin,

Thanks for reply.

using pdbgmx i generated charmm27 force field for protein
I prepared ligand topologies using swissparam online tool for all 5
ligands. But it worked for 4 and 5th one is creating problem at energy
minimization step.

Thanks
-sainitin



On Thu, Jul 4, 2013 at 9:02 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/4/13 3:00 PM, Sainitin Donakonda wrote:
>
>> Hi all,
>>
>> I have set of 5 different drugs which are complexed with same protein
>> (homology model). So i wanted to run MD simulation using gromacs. I
>> followed one procedure as follows
>>
>> 1) I took homology model and minimized it
>> 2) Then followed general procedure of simulation in gromacs.
>>
>> 4 drugs with same protein simulation was successful. Unfortunately 1 drug
>> among these 5 drugs  showing error at energy minimization step although i
>> used same em.mdp file which is used in other four simulations..
>>
>>
>> *Error :*
>> *
>> *
>> *708 particles communicated to PME node 2 are more than 2/3 times the
>>
>> cut-off out of the domain decomposition cell of their charge group in
>> dimension x.*
>> *This usually means that your system is not well equilibrated*
>> *
>>
>> *
>> This means system blowing up at energy minimization step itself ..just I
>> dont know whats the problem..
>>
>> Can anybody tell me how to solve this issue..major problem here is same
>> energy minimization step using .mdp file as mentioned above .dont know why
>> this is failing for this particular protein-drug complex.
>>
>>
> How did you prepare the initial configurations?  How did you create the
> ligand topology?  One or the other is your problem.
>
> -Justin
>
>
>  em.mdp which i used in in all 5 simulations as follows
>>
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization ; Title of run
>> define                  = -DFLEX_TI3P    ; defines to pass to the
>> preprocessor
>> constraints             = none
>>
>> ; 7.3.3 Run Control
>> integrator              = steep         ; steepest descents energy
>> minimization
>> nsteps                  = 2000          ; maximum number of steps to
>> integrate
>> energygrps              = Protein LIG        ; group(s) to write to energy
>> file
>>
>> ; 7.3.5 Energy Minimization
>> emtol                   = 1000          ; [kJ/mol/nm] minimization is
>> converged when max force is < emtol
>> emstep                  = 0.01          ; [nm] initial step-size
>> dt                      = 0.002
>>
>>
>> ; 7.3.9 Neighbor Searching
>> nstlist                 = 5            ; [steps] freq to update neighbor
>> list
>> ns_type                 = grid          ; method of updating neighbor list
>> pbc                     = xyz           ; periodic boundary conditions in
>> all directions
>> rlist                   = 1.2           ; [nm] cut-off distance for the
>> short-range neighbor list
>> rlistlong               = 1.4           ; [nm] Cut-off distance from the
>> long-range neighbor list
>>
>> ; 7.3.10 Electrostatics
>> coulombtype             = PME           ; Particle-Mesh Ewald
>> electrostatics
>> rcoulomb                = 1.2           ; [nm] distance for Coulomb
>> cut-off
>>
>> ; 7.3.11 VdW
>> vdwtype                 = switch       ; twin-range cut-off with rlist
>> where rvdw >= rlist
>> rvdw                    = 1.2           ; [nm] distance for LJ cut-off
>> rvdw_switch             = 0.2           ; Start switching th LJ potential
>> DispCorr                = Ener          ; apply long range dispersion
>> corrections for energy
>>
>> ; 7.3.13 Ewald
>> fourierspacing          = 0.12          ; [nm] grid spacing for FFT grid
>> when using PME
>> fourier_nx              = 0
>> fourier_ny              = 0
>> fourier_nz              = 0
>> pme_order               = 4             ; interpolation order for PME, 4 =
>> cubic
>> ewald_rtol              = 1e-5          ; relative strength of
>> Ewald-shifted potential at rcoulomb
>> optimize_fft            = yes
>>
>>
>> Thanks,
>> sainitin
>>
>>
>>
>>
>> Thanks,
>> Sainitin
>>
>>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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