AMBER Archive (2008)

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

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Mon Apr 28 2008 - 00:18:50 CDT


Dear Ross,

Thanks for your guidance. I am sending the initial steps pasted below.

  NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -3.5466E+04     1.4283E+01     9.5163E+01     C27       730
                                                                                                                                                 
 BOND    =      209.4338  ANGLE   =      469.2041  DIHED      =      650.5386
 VDWAALS =     3989.1824  EEL     =   -39295.7739  HBOND      =        0.0000
 1-4 VDW =      227.7164  1-4 EEL =    -1716.5737  RESTRAINT  =        0.0000
                                                                                                                                                 
                                                                                                                                                 
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    100      -4.2473E+04     2.3669E+00     2.6414E+01     C21       742
                                                                                                                                                 
 BOND    =     2249.4095  ANGLE   =      202.6472  DIHED      =      578.6509
 VDWAALS =     3620.4154  EEL     =   -47628.7490  HBOND      =        0.0000
 1-4 VDW =      205.3005  1-4 EEL =    -1710.5429  RESTRAINT  =        9.8252
 EAMBER  =   -42482.8685


I feel the problem could be in defining atoms atom types in the leap because it gives following output on using addatomtypes command:

> addatomtypes{{'SE1' 'SE' 'sp2'}{'SE2' 'SE' 'sp2'}}
addAtomTypes: type 'SE1' - max length is 2
addAtomTypes: type 'SE2' - max length is 2
> addatomtypes{{'SE' 'SE' 'sp2'}}
addAtomTypes: type 'SE' - max length is 2

Is this an incorrect way?

If you suggest I can send initial structure and charges to you I have derived from Gamess for ligand.

Thank you once again,

saurabh

--- On Sun, 27/4/08, Ross Walker <ross@rosswalker.co.uk> wrote:
From: Ross Walker <ross@rosswalker.co.uk>
Subject: RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
To: amber@scripps.edu
Date: Sunday, 27 April, 2008, 11:29 AM

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@scripps.edu [mailto:owner-amber@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

 

From Chandigarh to Chennai - find friends all over India. Click here. ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu


Bollywood, fun, friendship, sports and more. You name it, we have it. ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu