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| Dear Amber Users, I am trying to simulate nucleotide ligand complex. But It aborted during the simulation once I reduce the restraints below 20 in the input file and gives the following error. NSTEP ENERGY RMS GMAX NAME NUMBER 900 NaN NaN 0.0000E+00 H5T 1 BOND = NaN ANGLE = NaN DIHED = NaN VDWAALS = -140.5901 EEL = NaN HBOND = 0.0000 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN EAMBER = NaN NSTEP ENERGY RMS GMAX NAME NUMBER 1000 NaN NaN 0.0000E+00 H5T 1 BOND = NaN ANGLE = NaN DIHED = NaN VDWAALS = -140.5901 EEL = NaN HBOND = 0.0000 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN EAMBER = NaN .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... .... RESTARTED DUE TO LINMIN FAILURE ... The same nucleotide I have simulated with different ligands and those run fine. This ligand is having two Selenium atoms (which is not defined in the leap). Is this the reason for the problem? Every time it is stopping, and I am unable to solve it. Please help me in this regard. saurabh |