[gmx-users] strange structure after energy minimization

[Albert]

Dear Justin,

Thanks a lot for your information.

Can we do something in Gromacs to prevent this happen? Building 50 aa for a
disorder section is very challenging which may result in too many
artifices.

thanks a lot

Albert

On Sun, Oct 27, 2019 at 1:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/27/19 7:42 AM, Albert wrote:
> > Hello,
> >
> > I've performed a energy minimization in Gromacs 2018v4. The structure
> > looked very strange after energy minimization:
> >
> > There is a big gap in the structure for residue 400-450, which is missing
> > in the initial crystal structure. After energy minimization, gromacs
> > connected residue 399 to 451 with a covalent bond. Here is a screenshot
> for
> > the structure before and after the energy minimization:
> >
> > http://www.gpcrm.org/tmp/gmx/1.jpg
> >
> > I am just wondering how shall we solve this problem?
>
> Build in the missing residues before trying to create the topology.
> pdb2gmx probably warned you about a long bond when you generated the
> topology; it will happily add bonds between any residues in the system
> without any regard for missing intervening residues. You have to take
> care of those somehow.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
> Virginia Tech Department of Biochemistry
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>
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