Because it uses the atom index, which is most likely NOT the same as your processed file will not contain certain hydrogens, which are present in A.pdb.
24 aug 2012 kl. 16.33 skrev Hsinlin: > Thank you for your reply. > I checked the coordinates of all C-alpha atoms between two .pdb files. > They are exactly the same. > So I don't understand why g_rms(g_rmsdist) selecting group C-alpha give me > high values. > > Sincerely yours, > Hsin-Lin > > Erik Marklund wrote >> >> Hi, >> >> Since gromos-forcefields are not strictly all-atom forcefields, there >> might be a mismatch between atoms in the two structures. >> >> Best, >> >> Erik >> >> 24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang: >> >>> Hi, >>> >>> For example, I have a A.pdb as a initial structure file. >>> And I just used pdb2gmx on it to generate another B.pdb file with >>> GROMOS96 43a1 as its force filed. >>> Then I select C-alpha atoms to calculate RMSD. >>> echo 3 | g_rms -f B.pdb -s A.pdb >>> I suppose the RMSD value should be 0, but the value is high to about >>> 0.5nm. >>> Can someone explain for me? >>> >>> Sincerely yours, >>> Hsin-Lin >>> >>> -- >>> gmx-users mailing list gmx-users@ >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Only plain text messages are allowed! >>> * 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-request@. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> ----------------------------------------------- >> Erik Marklund, PhD >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: +46 18 471 6688 fax: +46 18 511 755 >> erikm@.uu >> http://www2.icm.uu.se/molbio/elflab/index.html >> >> -- >> gmx-users mailing list gmx-users@ >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Only plain text messages are allowed! >> * 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-request@. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/g-rms-and-g-rmsdist-on-initial-structure-tp5000492p5000496.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
