[gmx-users] mdp file problem

[Justin A. Lemkul]

madhumita das wrote:
> 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 

Probably.  Parameterizing such a species properly is not trivial, if it can even 
be done in a non-polarizable MM force field.

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

> to also know can I use amber forcefield in GROMACS for pdb files of lipid?
> 

Lipids probably aren't built in, but could potentially be added if you provide 
the proper parameters.  CHARMM is probably a better choice.  CHARMM27 is built 
into Gromacs already, and CHARMM36 is available as a download from the website.

-Justin

> On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://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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-- 
========================================

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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================