Hello users, I am trying to check wether my prepared system is ready to be put into a simualtion. I have a 2 body system 1protein + 1peptide. I have prepared the peptide using PRODRG server and included it into the protein .top file. I wanted to do a dummy minimization run with my prepared protein using 1step of CG. I am noticing that the protein portion (not the peptide/ligand) undergoes a shift in the X coordinate only between the input and output structures. All of the X coordinates are shifted by 40.37 units. e.g. 1 -18.608 to 21.767. I have used an mdp file from a tutorial.
following is the .mdp file and excerpts from the input and output structure files. Could you please give me your suggestions as to what is possibly happening here.Thanks in advance..Prasenjit #### .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 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 #### input structure file excerpt #### ATOM 1 N MET A 1 -18.608 9.660 16.832 1.00 0.00 ATOM 2 H1 MET A 1 -19.259 9.669 17.591 1.00 0.00 ATOM 3 H2 MET A 1 -19.007 10.131 16.045 1.00 0.00 ATOM 4 H3 MET A 1 -18.399 8.714 16.583 1.00 0.00 ATOM 5 CA MET A 1 -17.356 10.354 17.244 1.00 0.00 ATOM 6 CB MET A 1 -16.746 9.633 18.448 1.00 0.00 ATOM 7 CG MET A 1 -17.079 10.403 19.728 1.00 0.00 ATOM 8 SD MET A 1 -16.154 11.959 19.754 1.00 0.00 ATOM 9 CE MET A 1 -17.575 13.069 19.606 1.00 0.00 ATOM 10 C MET A 1 -16.359 10.341 16.082 1.00 0.00 ATOM 11 O MET A 1 -15.160 10.335 16.280 1.00 0.00 ATOM 12 N SER A 2 -16.845 10.337 14.871 1.00 0.00 ATOM 13 H SER A 2 -17.835 10.343 14.729 1.00 0.00 ATOM 14 CA SER A 2 -15.924 10.324 13.699 1.00 0.00 #### output structure file excerpt #### ATOM 1 N MET A 1 21.767 9.661 16.834 1.00 0.00 ATOM 2 H1 MET A 1 21.115 9.669 17.591 1.00 0.00 ATOM 3 H2 MET A 1 21.367 10.131 16.045 1.00 0.00 ATOM 4 H3 MET A 1 21.975 8.714 16.583 1.00 0.00 ATOM 5 CA MET A 1 23.016 10.351 17.241 1.00 0.00 ATOM 6 CB MET A 1 23.626 9.633 18.449 1.00 0.00 ATOM 7 CG MET A 1 23.295 10.400 19.728 1.00 0.00 ATOM 8 SD MET A 1 24.217 11.965 19.755 1.00 0.00 ATOM 9 CE MET A 1 22.803 13.067 19.607 1.00 0.00 ATOM 10 C MET A 1 24.015 10.341 16.085 1.00 0.00 ATOM 11 O MET A 1 25.218 10.335 16.282 1.00 0.00 ATOM 12 N SER A 2 23.529 10.337 14.867 1.00 0.00 ATOM 13 H SER A 2 22.540 10.343 14.726 1.00 0.00 ATOM 14 CA SER A 2 24.447 10.323 13.699 1.00 0.00 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