AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...

From: saurabh agrawal <imsam100.yahoo.co.in>
Date: Sat, 26 Apr 2008 17:06:13 +0530 (IST)
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


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