[gmx-users] Simulation of wild and mutant types of HSA protein

Francesco Carbone fra.carbone8 at gmail.com
Tue Jun 3 14:29:40 CEST 2014

hi Negar,
I'm doing a similar work, but with another protein and what I did was to
mutate the wild-type using mutmodel (Martin et al., 2002).
In my case I had more than 200 mutants and only the wt pdb was available.



On 3 June 2014 13:19, Negar Parvizi <negar.parvizi at yahoo.com> wrote:

> Dear Gromacs users
> >
> >I have a question about protein simulation in Gromacs. We are interested
> in the effect of single point mutation on the structure of HSA (human serum
> albumin) protein.
> >
> >We selected a pdb file for wild type HSA and submitted it for MD
> simulation.
> >One of the mutatns of HSA is called R218H. To simulate this mutant which
> of the following ways is correct?
> >
> >1) we found a pdb file for this mutant. It has 14 residues missed which
> we used modeller to add these residues. Now we
> >can simulate this protein.
> >
> >2) One of our friends suggested to take the wild type HSA and only
> substitute the residue 218 to create the mutant form of HSA and to use
> swiss pdb viewer to get the appropriate pdb file for that.
> >
> >Now I wanted to know which way is correct? is there any difference
> between these two approaches?
> >Is it necessary to take the pdb file for the mutant and add the missed
> residues or only with the substitution of that single residue in the wild
> type HSA pdb file we can make the mutant pdb file?
> >
> >Your prompt response would be greatly appreciated.
> >Thanks
> >D.M
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