[gmx-users] strange structure after energy minimization

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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