[gmx-users] minimization is not converging (Bratin Kumar Das)

[Bratin Kumar Das]

Dear ABEL,
                   I tried CHARMM-gui but the charmm gui is getting failed
for my system.


On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hi
>
> Did you try to use CHARMM-gui and use the gromacs files generated for this
> system to see if your problem is resolved?
>
> Stéphane
>
> ------------------------------
>
> Message: 5
> Date: Thu, 6 Sep 2018 19:55:07 +0530
> From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] minimization is not converging
> Message-ID:
>         <CAM7TW5vtko_7pev_5mTEHT4_WX9ps82Vaw+0=A6HjAtAg5xamw@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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