[gmx-users] How to find the mutation effect?

[Thales Kronenberger]

Dear Fugui

I have faced the same problem in the begining of my projects with site
direct mutagenesis, until I realized that even if the RMSD is looking
similar the RMSF can show small statitical significant changes.

Where in the protein is the mutation? depending on where is in the
structure you can propose different analyses such as hydrogen bonding
counting (if in the active site) or even hidrophobicity pattern (for
interface mutations).

Best regards
Thales


2013/12/15 xiao <helitrope at 126.com>

> Dear all,
>
> I am doing a MD on a mutant protein which is unstable from exprient.
> However, i found no difference between the wild type and the mutant protein
> from md, the structure and the rmsd are very similar in the mutant and the
> wild type.
>
> Can anyone tell me how to tackle this problem?
>
> Best regards
>
> Fugui
> --
> 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-request at gromacs.org.
>