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 <luc...@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: luc...@mails.tsinghua.edu.cn > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.