Mark and other users, Thanks for the input. I understand that translation does not have any effect on the energy calculations since the point of reference is the protein itself. The problem over here is that if a translation operation is to be done it should perform the same operation on all the X,Y or Z coordinates. A brief summary of the job - i have a protein + peptide system which i want to simulate. I have generated peptide itp file using PRODRG and included in the protein .top file. I am doing a dummy mdrun to check the system. I have added excerpts from the structure files and the .mdp file.The first is the input structure file for grompp > .trp file > mdrun while the second is the output of the mdrun.Comparing the two structures whats happening is that for the protein coordinates (till 1895) a tranlation is being performed only on the protein X coordinates while for the peptide the translation is being performed only on the Y and Z coordinates. This results in the peptide and protein to be placed separate from each other.Please help me with your suggestions. Thanks in advance
#### input structure #### ATOM 1890 CD2 HIS A 181 17.104 -17.966 35.020 1.00 0.00 ATOM 1891 CE1 HIS A 181 15.979 -16.114 34.942 1.00 0.00 ATOM 1892 NE2 HIS A 181 17.022 -16.732 34.381 1.00 0.00 ATOM 1893 C HIS A 181 15.328 -21.621 37.119 1.00 0.00 ATOM 1894 O1 HIS A 181 14.341 -22.372 36.561 1.00 0.00 ATOM 1895 O2 HIS A 181 15.818 -21.755 38.381 1.00 0.00 TER HETATM 1 NAA DRG 182 3.259 -11.741 -15.248 1.00 20.00 HETATM 2 HAA DRG 182 2.868 -11.170 -15.970 1.00 20.00 HETATM 3 HAB DRG 182 4.140 -12.104 -15.551 1.00 20.00 HETATM 4 HAC DRG 182 2.637 -12.498 -15.050 1.00 20.00 HETATM 5 CAB DRG 182 3.456 -10.923 -14.017 1.00 20.00 HETATM 6 CAC DRG 182 4.054 -11.797 -12.913 1.00 20.00 HETATM 7 OAD DRG 182 3.478 -12.789 -12.512 1.00 20.00 HETATM 8 N DRG 182 5.208 -11.438 -12.418 1.00 20.00 HETATM 9 HAD DRG 182 5.666 -10.619 -12.763 1.00 20.00 HETATM 10 CA DRG 182 5.843 -12.248 -11.340 1.00 20.00 #### output structure #### ATOM 1890 CD2 HIS A 181 57.476 -17.958 35.022 1.00 0.00 ATOM 1891 CE1 HIS A 181 56.353 -16.113 34.945 1.00 0.00 ATOM 1892 NE2 HIS A 181 57.395 -16.742 34.389 1.00 0.00 ATOM 1893 C HIS A 181 55.696 -21.634 37.130 1.00 0.00 ATOM 1894 O1 HIS A 181 54.730 -22.362 36.575 1.00 0.00 ATOM 1895 O2 HIS A 181 56.185 -21.754 38.363 1.00 0.00 ATOM 1896 NAA DRG B 182 3.259 41.631 44.612 1.00 0.00 ATOM 1897 HAA DRG B 182 2.868 42.201 43.887 1.00 0.00 ATOM 1898 HAB DRG B 182 4.140 41.267 44.306 1.00 0.00 ATOM 1899 HAC DRG B 182 2.637 40.873 44.807 1.00 0.00 ATOM 1900 CAB DRG B 182 3.456 42.447 45.837 1.00 0.00 ATOM 1901 CAC DRG B 182 4.052 41.573 46.943 1.00 0.00 ATOM 1902 OAD DRG B 182 3.475 40.579 47.344 1.00 0.00 ATOM 1903 N DRG B 182 5.210 41.933 47.440 1.00 0.00 ATOM 1904 HAD DRG B 182 5.668 42.752 47.095 1.00 0.00 ATOM 1905 CA DRG B 182 5.844 41.127 48.515 1.00 0.00 #### .mdp file #### cpp = /usr/bin/cpp constraints = none integrator = cg nsteps = 1 emtol = 100.0 emstep = 0.01 nstcomm =1 ns_type = grid morse = no ; was given as yes in tutorial coulombtype = shift vdw_type = shift rlist = 1.4 rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php