Hi all, I'm trying to run the simulation of a proline with an acetyl group on the N terminus and an NH2 on the C. I've already chenged the name of the residues on the pdb file, this way: HETATM 1 N PRO 1 -0.650 -0.337 0.028 HETATM 2 CA PRO 1 0.700 -0.304 -0.532 HETATM 3 HA PRO 1 0.634 -0.117 -1.630 HETATM 4 CB PRO 1 1.186 -1.746 -0.265 HETATM 5 HB1 PRO 1 1.743 -1.795 0.701 HETATM 6 HB2 PRO 1 1.848 -2.144 -1.071 HETATM 7 CG PRO 1 -0.109 -2.560 -0.104 HETATM 8 HG1 PRO 1 0.043 -3.520 0.445 HETATM 9 HG2 PRO 1 -0.525 -2.790 -1.115 HETATM 10 CD PRO 1 -1.046 -1.592 0.637 HETATM 11 HD1 PRO 1 -2.109 -1.878 0.465 HETATM 12 HD2 PRO 1 -0.827 -1.548 1.730 HETATM 13 C PRO 1 1.650 0.724 0.080 HETATM 14 O PRO 1 2.846 0.576 0.058 HETATM 15 N NH2 1 1.140 1.851 0.659 HETATM 16 H1 NH2 1 0.142 2.048 0.638 HETATM 17 H2 NH2 1 1.837 2.497 1.025 HETATM 18 CH3 ACE 1 -2.970 0.591 0.323 HETATM 19 HH31 ACE 1 -2.983 0.374 1.415 HETATM 20 HH32 ACE 1 -3.524 1.545 0.167 HETATM 21 HH33 ACE 1 -3.526 -0.201 -0.227 HETATM 22 C ACE 1 -1.543 0.704 -0.194 HETATM 23 O ACE 1 -1.220 1.712 -0.778
Every's fine till I try to use the command mdrun, after preprocessing with gromp with the pr.mdp. I get this error: 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 .. 125 ] How could I solve the problem? Should I modify something else other than the pdb? Thanks in advance Mauro Puppett _________________________________________________________________ Scarica GRATIS la versione personalizzata MSN di Internet Explorer 7! http://optimizedie7.msn.com/default.aspx?mkt=it-it_______________________________________________ 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
