Dear gmx-users, I'm simulating a homodimeric protein obtained by homology modelling. In the .pdb file, I have 2 chain identifiers (A and B). I used Gromacs 4.0.7 to prepare the .gro files for simulation (up to nvt); then I was forced to switch to Gromacs 4.5.4 on another machine to continue with npt and full MD. I used the files from Gromacs 4.0.7 to continue, and it seems to me that all went OK. Now I have the files from the full MD, and I started to analyze them. I used g_rmsf to analyze the fluctuations of the residues, and I found that the results for the two subunits of the protein are superimposed. In the file .gro that comes from the MD as well as in the file .gro that comes from the npt MD made with Gromacs 4.5.4, the number of residues of the second subunit does not continue after the first subunit (i.e. after the last 359th residue of the first subunit, I see that the first residue of the second subunit is numbered 1 instead of 360), but in the nvt file produced by Gromacs 4.0.7 that I provided to Gromacs 4.5.4, the numbering of the two subunits is sequential. My questions are: 1) why Gromacs 4.5.4 changed the numbering of the residues in the two subunits, even if it started from a .gro file? 2) Does this affect the result of the MD? 3) how can I separate, or renumber, the resulting .gro files in order to have a graph in which the fluctuations are not superimposed? Thank you very much and regards Anna __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: [email protected] Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano)
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
