[gmx-users] Potential energy of protein after energy minimization

[Subhashree Rout]

Hello Sir
I have generated the structure using PHYRE server, performed its structural
validations. As per your suggestion I have checked the protein in both
visualizing software. During MD simulation of the protein, the pdb2gmx is
generating topol.top and .itp without any errors.
Do I need to check the structure with other protein prediction server or
software for 3D structure?



On Thu, Feb 18, 2016 at 3:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> There's something catastrophically wrong with your input structure. Look it
> with a visualization program, e.g. VMD, PyMol
>
> Mark
>
> On Thu, Feb 18, 2016 at 10:39 AM Subhashree Rout <
> subhashree.rout at kiitbiotech.ac.in> wrote:
>
> > Hii
> >
> > I am simulating protein (PfCDPK5) in water. After performing energy
> > minimization, the potential energy of my protein is 2.86082e+07. As
> > mentioned in the tutorial
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
> > ,
> > the Epot should be negative.
> >
> > The em.mdp file-
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator    = steep        ; Algorithm (steep = steepest descent
> > minimization)
> > emtol        = 1000.0      ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep      = 0.01      ; Energy step size
> > nsteps        = 50000          ; Maximum number of (minimization) steps
> to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist            = 1            ; Frequency to update the neighbor list
> > and long range forces
> > cutoff-scheme   = Verlet
> > ns_type            = grid        ; Method to determine neighbor list
> > (simple, grid)
> > coulombtype        = PME        ; Treatment of long range electrostatic
> > interactions
> > rcoulomb        = 1.0        ; Short-range electrostatic cut-off
> > rvdw            = 1.0        ; Short-range Van der Waals cut-off
> > pbc                = xyz         ; Periodic Boundary Conditions (yes/no)
> >
> > Kindly suggest where I am going wrong.
> >
> > --
> > Subhashree Rout
> > PhD Scholar
> > Bioinformatics Lab
> > KIIT School of Biotechnology
> > KIIT University
> > Bhubaneswar
> > Odisha
> > INDIA
> > Pin-751024
> > --
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-- 
Subhashree Rout
PhD Scholar
Bioinformatics Lab
KIIT School of Biotechnology
KIIT University
Bhubaneswar
Odisha
INDIA
Pin-751024