[gmx-users] Crashes during protein-ligand simulation

[James Starlight]

Justin,

unfortunately my last system have also been crashed after 35ns of
simulation with the links warnings accompanied by the error

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

This time I've devided all functional groups of my ADENOSINE ligand
into separate charge groups in topol.itp.

;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    NT    1    ADN     N6    1   -0.844  14.0067
    2     H    1    ADN    H11    1    0.422   1.0080
    3     H    1    ADN    H12    1    0.422   1.0080      ;  0.000
    4     C    1    ADN     C8    2    0.097  12.0110
    5    HC    1    ADN    H01    2    0.177   1.0080
    6    NR    1    ADN     N3    2   -0.642  14.0067
    7     C    1    ADN     C4    2    0.175  12.0110
    8     C    1    ADN     C5    2    0.092  12.0110
    9    NR    1    ADN     N7    2   -0.556  14.0067
   10     C    1    ADN     C6    2    0.657  12.0110      ;  0.000
   11     C    1    ADN    C5'    3   -0.677  12.0110
   12     C    1    ADN    C4'    3    0.834  12.0110
   13    OE    1    ADN    O4'    3   -0.248  15.9994
   14     C    1    ADN    C1'    3   -0.558  12.0110
   15     C    1    ADN    C2'    4    0.603  12.0110
   16     C    1    ADN    C3'    5   -0.212  12.0110
   17    NR    1    ADN     N9    3    0.415  14.0067
   18    OA    1    ADN    O2'    4   -0.606  15.9994
   19     H    1    ADN    H08    4    0.482   1.0080
   20    OA    1    ADN    O3'    5   -0.606  15.9994
   21     H    1    ADN    H06    5    0.482   1.0080
   22    OA    1    ADN    O5'    3   -0.246  15.9994
   23     H    1    ADN    H03    3    0.337   1.0080      ; -0.000
   24     C    1    ADN     C2    6    0.502  12.0110
   25    HC    1    ADN    H10    6    0.106   1.0080
   26    NR    1    ADN     N1    6   -0.608  14.0067      ;  0.000


Also I've done proper equilibration in tho steps (I've used 1fs
integrator steps on both stages of equilibration)
1- I've made equilibration with posres ( 500ps) on protein backbone
atoms as well as ligand with x-ray water

2- The next step (5ns) was done without posres only with smaller
integrator steps.

What another possible sollutions could be ?

James

2012/7/7, Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> On 7/7/12 11:08 AM, James Starlight wrote:
>> justin,
>>
>> It seems that problem was in the big charge groups in the ligand.itp
>> file. In particularly I've devided largest group into several smaller
>> and there haven't any crashes been occured yet.
>>
>> With my last system with the the default COM group I've obtained crash
>> on the 25ns with the error about ligand's big cngr exactly.
>>
>>
>> By the way could you tell me how I could analyse stability of the
>> protein-ligand system as well as contributions of the individual
>> non-covalent contacts with the .EDR file?
>>
>> In my mdp file I've defined energygrps= Protein Ligand   as the
>> separate energy terms.
>>
>> During analysis of the edr file I've observed some options like
>> LJ-SR:Protein-ADN     ( this value was slightly negative (-100) during my
>> trr )
>> Coul-14:Protein-ADN ( this value was constantly zero )
>> Coul-SR:ADN-rest ( this value was equal to the LJ-SR:Protein-ADN  -100 )
>>
>> What conclusions in general could I do based on that values ? How I
>> could measure stability of the ligand ( beside dirrect RMSD
>> measurement) from such energy terms?
>>
>
> In isolation, these values are not indicative of anything.  Their absolute
> values are completely dependent upon the parameters set in the topology.
> Force
> field parameterization methodology does not require that any topology
> reproduce
> protein-ligand energetics; only true free energy calculations might tell you
> this.
>
> In conjunction with other metrics (hydrogen bonding, contacts, RMSD, SASA,
> etc)
> you may be able to make some meaningful observations about ligand stability
> in
> the protein binding site.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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