<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi everyone, <br>I am trying to run a simulation on a xray structure that has 15 residues missing. I have made the topology file accordingly. But after energy minimization, the residues between which the portion is missing, got connected. I tried an energy minimization with all-bonds constraint, but that i guess did not do it properly. <br>This is the last part of the minimization run <br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 1000<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br><br>writing lowest energy coordinates.<br><br>Back Off! I just backed up ccpox_em.trr to ./#ccpox_em.trr.1#<br><br>Back Off! I just backed up
ccpox_b4pr.pdb to ./#ccpox_b4pr.pdb.1#<br><br>Steepest Descents converged to machine precision in 15 steps,<br>but did not reach the requested Fmax < 1000.<br>Potential Energy = -2.2785961e+05<br>Maximum force = 5.1547680e+08 on atom 1004<br>Norm of force = 8.2600877e+08<br><br>My question is how can I run a simulation on these structure keeping that part as it is?<br><br>Thanking you in advance.<br>Abhik<br><br><br><br> <br><br><div><div><div><font size="3" face="system"><strong>Abhik Mukhopadhyay<br> </strong></font></div><font size="3"><font size="3"><font size="2"><span style="font-weight: bold;"> Departamento Química / Faculdade de Ciências e Tecnologia </span><br style="font-weight: bold;"><span style="font-weight: bold;"> Universidade Nova de Lisboa , 2829-516 Caparica, Portugal </span><br style="font-weight: bold;"><span style="font-weight:
bold;"></span></font></font><br>Mob. 00351912991251<br></font><font size="3"> <a rel="nofollow" target="_blank" href="http://xtal.dq.fct.unl.pt/"> http://xtal.dq.fct.unl.pt/</a><br></font><br></div></div></td></tr></table><br>