[gmx-users] mdp file problem
madhumita.bioinfo at gmail.com
Tue Nov 8 18:13:47 CET 2011
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=
>> 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
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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