Hi Igor, Please look at the contents of the files. Note the order of atoms.
Cheers, Tsjerk On Jan 24, 2012 7:31 PM, "192.168.100.1" <shch...@bpci.kiev.ua> wrote: ** Hi, I applied *pdb2gmx* to PDB file *A.pdb* with force field *gromos53a5* and water model *spc* and then compared the resulting *A.gro* file with initial PDB one, using program *g_rmsdist* by the following command: * /opt/software/gromacs/gromacs-4.5.3-intel/bin/g_rmsdist -f A.gro -s /home/shch406/PDB/A.pdb -o A.dA.xvg * Structures appeared to be quite different - RMSD = 1.67! *@ subtitle "of distances between Protein atoms"* *0 1.67265* Why? Thanks in advance, Igor -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
