Hello All,<br><br>I was trying to run a MD simulation of a 17 amino acid peptide. At the position restraint step, the program crashed after running ~536 ps.<br><br>It gave the error message:<br><br>"t=536.242 ps: Water molecule starting at atom 6101 cannot be settled.<br>
Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates."<br><br>So I looked into the pdb files for atom 6101:<br><br>In the last but one step, the pdb file looks like:<br>
<br>ATOM 6101 OW SOL 1970 44.896 30.613 17.849 1.00 0.00<br>ATOM 6102 HW1 SOL 1970 45.375 30.296 18.668 1.00 0.00<br>ATOM 6103 HW2 SOL 1970 44.264 29.904 17.537 1.00 0.00<br><br>In the last step, the pdb file looks like:<br>
<br>ATOM 6101 OW SOL 1970 395154652137521152.000-290190255628222464.000695407981780533248.000 1.00 0.00<br>ATOM 6102 HW1 SOL 1970 -2104656020830683136.0005806908484133847040.000-6427192471385538560.000 1.00 0.00<br>
ATOM 6103 HW2 SOL 1970 1131095442881249280.000593978790032441344.0001018902650772520960.000 1.00 0.00<br><br>So, there is clearly something wrong. What should I do now to solve this problem?<br><br>Thanks,<br>Sayan.<br clear="all">
<br>-- <br> Sayan Bagchi <br><div><br></div><br>