Dear gmx-users<br> We want to study interaction of ligand to enzyme. We constructed the gro and top file from Prodrg and add it to the end of enzyme gro and change the number of atoms. Some of calculation carried out until mdrun of pr.mdp, but in this step we encontered to following error. what is the cause of it and how we can solve it.<br> Thanks a lot of.<br> <br> tep 5, time 0.01 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> max 0.007443 (between atoms 3555 and 3557) rms 0.000281<br> bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 506 507 30.0 0.0999 0.0999 0.1000<br> 1861 1862 37.0 0.0999 0.1000 0.1000<br> 2131 2132
30.4 0.0999 0.0999 0.1000<br> 2604 2605 35.4 0.0989 0.0997 0.1000<br> 2997 2998 36.5 0.0999 0.1000 0.1000<br> <br> t = 0.010 ps: Water molecule starting at atom 12011 can not be settled.<br> Check for bad contacts and/or reduc<br> <br> <br> <p>
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