[gmx-users] Mutation

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Wed Sep 26 22:06:36 CEST 2018

    You can go directly with pgb2gmx to create the topology of your mutated
structure. Hope, you did mutation in pymol. If any fatal error came then
you have to edit the atom types of the particular amino acid, as it is
defined in the particular .rtp file of chosen force field. I hope your
problem will be solved.

On Thu, Sep 27, 2018, 1:30 AM Mohammad Goodarzi <mohammad.godarzi at gmail.com>

> Hello,
> I am trying to check for stability of a protein based on single point
> mutation. I follow the protocol as described here
> http://pmx.mpibpc.mpg.de/tutorial_peptide/index.html
> basically I can do folded one and calculate the delta G but for unfolded I
> don't know how to do that. is there anyone could give me some advise on how
> to initiate the structure ? I believe the rest of the analysis is the same
> but my problem is only the creation of topology and structure of it.
> Thanks,
> Mo
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