[gmx-users] Complementing the missing resideus of the protein

[Sudip Das]

Hi Chenlin,

You can use molecular dynamics flexible fitting (MDFF or xMDFF) protocol.

https://www.ks.uiuc.edu/Research/mdff/

Regards,
Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India


On Fri, Oct 5, 2018 at 10:24 AM Chenlin Lu <lucl13 at 163.com> wrote:

> Hello all,
>
>
> I am working on a protein engineering project. A protein mutant (some )
> was obtained and X-ray crystallography was applied to deterine the crystal
> structure. Unfortunately, there are some residues with high overlap
> electrodensity, which means the structure of these residues could not be
> determined. So, my plan is to use MD to analyis the relation of flexibility
> and Amino acis squences for mutant part for further experiment. As a
> reslut, I am wondering if there is some way to complement (or initial
> generate the configuration) the missing part of the protein in order to do
> MD simulation. Could anyone help me? Thx in advance.
>
>
> Best,
> Chenlin
>
> --------------------------------------------------
>
> Chenlin Lu
>
> Department of Chemical Engineering,
>
> Tsinghua University, Beijing, 100084
>
> Tel: 86-13120180517
>
> Email: lucl17 at mails.tsinghua.edu.cn
>
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