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

Sudip Das das.sudip37 at gmail.com
Fri Oct 5 08:45:41 CEST 2018

Hi Chenlin,

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


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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