Dear Justin, to add other elements to find a solution to this problem, I repeated all the Gromacs procedure until minimization on the file PDB I used as template to model my protein. pdb2gmx warns that 232 atoms have non-zero occupancy, it's because there are sidechains with alternative conformations, but for the rest everything is OK. When I try to launch the mdrun to minimize the protein, however, the range checking error appears: Reading file 1WBE_min.tpr, VERSION 4.0.7 (double precision)
Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 ------------------------------------------------------- Program mdrun_d, VERSION 4.0.7 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ] So I think definitely that the problem is in the protein structure arising from some bad coordinates in the template I used to model my protein. I have to wait for the approval of people working on this project to send you coordinates and topologies of my model, but since I think that the error in the model is strictly derived from the error in this public file, I will send you privately the coordinates and topologies of this file. Please remember that in my model there are some atoms with occupancy <1, but the conformation of the sidechains is unique. I corrected by hand the occupancy on my model, re-tried to minimize it and nothing changed: the same error occurs. On the contrary, in this case, with this template file, the mdrun did not start at all. Once again thank you very much and best regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito"
-- 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/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/mailing_lists/users.php
