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

Negar Parvizi negar.parvizi at yahoo.com
Thu Jun 5 08:10:16 CEST 2014

Dear Francesco,

Thank you so much for your help.
Could you please explain me more about this software and what you are doing for modeling mutants from wt pdb?
In my job we want to check RMSD, solvent accessible surface area and gyration radius. Would you please say what properties you check when you are dealing with single point mutations?


On Tuesday, June 3, 2014 4:59 PM, Francesco Carbone <fra.carbone8 at gmail.com> wrote:

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.
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