[gmx-users] bad contacts and/or reduc

[davood ajloo]

Dear gmx-users
 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.
 Thanks a lot of.
 
 tep 5, time 0.01 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 max 0.007443 (between atoms 3555 and 3557) rms 0.000281
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
     506    507   30.0    0.0999   0.0999      0.1000
    1861   1862   37.0    0.0999   0.1000      0.1000
    2131   2132   30.4    0.0999   0.0999      0.1000
    2604   2605   35.4    0.0989   0.0997      0.1000
    2997   2998   36.5    0.0999   0.1000      0.1000
 
 t = 0.010 ps: Water molecule starting at atom 12011 can not be settled.
 Check for bad contacts and/or reduc
 
 
 
		
---------------------------------
Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060526/c0b26a58/attachment.html>