[gmx-users] problem in simulation mutant p53 protein both in swiss pdb viewer and energy minimization with gromacs

[delara aghaie]

Dear Gromacs Users
I want to simulate human p53 protein and two of its mutants to see how mutation affect its structural properties.
I obtained the nature and mutant pdb files form protein data bank.
when I submitted the mutant files to pdb2gmx command it gave error on misiing atoms. I fixed the pdb files using swiss pdb viewer.
There is an optin in this program which minimizes the energy of pdb file, but when I wanted to minimize the energy of mutant pdb file, I got error. You can see the error in attached files. (I hhave attached the image of error page)

After seeing this error, I decided to ignore this stage and submit the mutant pdb file, taken from swiss pdb viewer to pdb2gmx command. When I did that, I did not get error and decided to acceot the energy minimization using gromacs instead of the swiss pdb viewer.
Now the questions:

1) how can I fix the error by swiss pdb viewer?
2) Is it right to take pdb file with out energy minimizing from swiss pdb viewer and submit it for simulation to gromacs?
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The nest problem is that when I submitted the mutant pdb file taken from swiss pdb to pdb2gmx and it worked successfully, then I made the simulation box and added the required ions according to hustin lyzozyme tutorial.
When I did energy minimization I got strange output files besides the regular ones:
the name of those files are:
step14b_n0.pdb
step14c_n0.pdb
step15b_n4.pdb
step15c_n4.pdb

....
It would be greatly appreciated if you let me know what are these files and what I should do about them?
can I continue the simulation by just ignoring them?

Thanks in advance
Best regards
D.M