AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Apr 27 2008 - 00:59:57 CDT

Dear Saurabh

 

The NaN’s essentially mean that certain energies are infinity. This normally occurs because you have a bad starting structure, often due to two atoms sitting on top of each other. Unfortunately seeing step 900 doesn’t help much. It would be much easier to see the very first step and see if any energies there are reported as NAN, or *’s or just very large. If you can post this it might be easier to see what is wrong. Part of the output on the step line lists the atom with the largest force. If there are problems with the structure this gives you an idea of the first place to look.

 

The two Selenium atoms are very concerning – where did you get the parameters for these? What did you do with them? Often selenium atoms are used by crystallographers as part of the structure solving and thus are not part of the structure in a biologically relevant context. I’m not sure though if they are additional or used to replace something else in the protein like zinc or iron. If they are just additional then you should probably just delete them. If they substituted something else then you will need to modify the pdb to change them to the correct atoms in the biological context. You’d then need to add the missing parameters for these atoms.

 

In the meantime please post the energies from step zero / one and also post more details about the structure and how you set it up, input file etc.

 

All the best

Ross

 

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of saurabh agrawal
Sent: Saturday, April 26, 2008 4:36 AM
To: amber users
Subject: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...

 

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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