[gmx-users] minimization is not converging

[Bratin Kumar Das]

Thank you sir

On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> > 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.
>
> It may, and I have already suggested a few things for you to check.
> Please do so.
>
> If you can provide more specific diagnostics of what is happening,
> someone on this list might be able to suggest something. What you've
> provided thus far is a generic instability that no one can diagnose.
> Investigate the structure, check for pdb2gmx warnings, follow the
> diagnostics I've already suggested, and report back with specific
> observations, a PDB code, and exact errors or warnings you get from any
> program if you need further help.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
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>
> jalemkul at vt.edu | (540) 231-3129
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>
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