[gmx-users] Re: mdp file problem

[madhumita das]

Dear Justin,

I could solve that perticular error but another problem has come, After
running energy minimization, the sulphur and mercury(GG)atoms (present in
the modified residue of cysteine named CYP at 182 position) break the bonds.

On Thu, Nov 10, 2011 at 7:28 PM, madhumita das
<madhumita.bioinfo at gmail.com>wrote:

> Dear Justin,
>
> I could resolve that perticular error but another problem has come, After
> running energy minimization, the sulphur and mercury(GG)atoms (present in
> the modified residue of cysteine named CYP at 182 position) break the bonds
> and become freely moving atoms. I have attached my prepared
> gromacs(aqp_newbox) topology(topol.top) and file obtained after energy
> mimization(em.gro).
>                                                     Please help me.
>
> Madhumita
>
>
> On Tue, Nov 8, 2011 at 5:03 PM, madhumita das <madhumita.bioinfo at gmail.com
> > 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
>>  The mdp file is attached.
>>
>>                                    Please help.
>>
>> Madhumita Das
>>
>>
>
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