[gmx-users] Energy minimization result problem

[Justin Lemkul]

On 4/11/14, 7:47 AM, neha_bharty wrote:
> Hello
> I am new user of gromacs. I am using gromacs 4.6.3
> I wanted to minimize the energy of a protein. Before energy minimization the
> prockeck result for Ramachandran plot was 89% in allowed region but after
> energy minimization the result become worse i.e. 87%.
> I was performing energy minimization to refine the model. But the model
> become worse after that.

That's not a huge change, nor is energy minimization rigorous enough to fully 
refine a model.  EM will probably optimize the side chains pretty well, but the 
backbone may require actual MD simulation to sample better conformations.  The 
changes that take place during EM are typically very small.

> I Model the protein using homology modeling and needed it for docking
>
> I am also doing it with different protein molecules but again the same
> problem occurs.
> I don't know that its normal or there is problem with my parameter or force
> field.
> I am also mentioning the detail of my energy minimization.
>
> The details are:
> Force Field Used: CHARMM27 all-atom force field
> Water Model: TIP3P
>

CHARMM36 may be a better option.  The recalibration of the CMAP terms could be 
relevant here.  See http://mackerell.umaryland.edu/CHARMM_ff_params.html to 
download the force field files.

-Justin

> em.mdp file is:
>
> ; VARIOUS PREPROCESSING OPTIONS =
> title                    =
> cpp                      = /lib/cpp
> include                  =
> define                   = -DFLEXIBLE
>
> ; RUN CONTROL PARAMETERS =
> integrator               = steep
> ; start time and timestep in ps =
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 15000
>
> ; ENERGY MINIMIZATION OPTIONS =
> emtol                    = 10
> emstep                   = 0.1
> nstcgsteep               = 1000
>
> coulombtype	=pme
> nstenergy	=10
>
> Please help me out for this.
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Re-Energy-minimization-result-problem-tp5015793.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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