[gmx-users] mdp file problem

[madhumita das]

Thanks Justin,

I must inform you that my pdb file has a modified cysteine residue having a
mercury atom attached to the sulphur atom next to the residue having the
atom 2700. Is the murcury atom creating any problem? I want to also know
can I use amber forcefield in GROMACS for pdb files of lipid?

On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> madhumita das wrote:
>
>>
>> Hi GROMACS users,
>>
>>    i am in the midst of simulating  a protein in water.  I have modified
>>  a residue  in my  pdb file at position  182,  using amber and then
>> acpype.py.  But  after running  the energy minimization step,using  em.mdp
>> file  generated from acpype , following error comes.
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.00000e+03
>>   Number of steps    =         5000
>> Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax=         inf, atom=
>> 2700
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 1000
>>
>> Double precision normally gives you higher accuracy.
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 18 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy  =  9.8982703e+17
>> Maximum force     =            inf on atom 2700
>> Norm of force     =  1.7474532e+19
>>
>
> An infinite force suggests severe atomic overlap.  Check the starting
> structure, paying close attention to atom 2700 and its surrounding
> environment.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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