[gmx-users] minimization is not converging

[Bratin Kumar Das]

Respected Dr. Justin
                                     To avoid the complicacy I solvated
only the protein pdb in a pbc box and tried for minimizatin. There also
minimization is not converging. Sir, till now I learned to carry out
protein ligand system md simulation successfully. I tried all possible ways
to simulate the my membrane protein system. I failed. Is it possible that
the PDB file itself have some serious issue with its coordinates. the
structure refinement is required may be.

On Thu, Sep 6, 2018, 7:24 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/6/18 9:51 AM, Bratin Kumar Das wrote:
> > Respected Dr Justin,
> >                                       I took one membrane protein pdb
> file
> > and converted it to .gro using pdb2gmx. Next I builded and packed the
> POPC
> > phospholipids bylayer using vmd membrane builder plugin. Subsequently I
> > solvated the system in vmd only. The entire system was converted to .gro
> > and all the water molecules and POPC molecules making bad contacts are
> > deleted. I added ions to nutralize the system in gromacs using genion.
> > Prior to that all the POPC topoloy properly included in topol.top. prior
> to
> > energy minimization all the steps ran with out fatal error. I followed
> the
> > procidure explained in gromacs tutorial. Evrey cases the same error is
> > coming during minimization.
>
> It's not worth moving on to a complicated membrane system when you said
> the protein itself does not minimize properly. Solve the easier problem
> first and work with just the protein. Only when you understand why that
> was unstable should you move on to the membrane system.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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On Sep 6, 2018 7:24 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:



On 9/6/18 9:51 AM, Bratin Kumar Das wrote:
> Respected Dr Justin,
>                                       I took one membrane protein pdb file
> and converted it to .gro using pdb2gmx. Next I builded and packed the POPC
> phospholipids bylayer using vmd membrane builder plugin. Subsequently I
> solvated the system in vmd only. The entire system was converted to .gro
> and all the water molecules and POPC molecules making bad contacts are
> deleted. I added ions to nutralize the system in gromacs using genion.
> Prior to that all the POPC topoloy properly included in topol.top. prior
to
> energy minimization all the steps ran with out fatal error. I followed the
> procidure explained in gromacs tutorial. Evrey cases the same error is
> coming during minimization.

It's not worth moving on to a complicated membrane system when you said
the protein itself does not minimize properly. Solve the easier problem
first and work with just the protein. Only when you understand why that
was unstable should you move on to the membrane system.


-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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

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