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? ------------- 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 -- 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-requ...@gromacs.org.
