AMBER Archive (2003)

Subject: Re: AMBER: atomic clash or structure size?

From: Qiang Lu (qiangl_at_uci.edu)
Date: Tue Sep 02 2003 - 16:20:32 CDT

Hi atobak,

I was in the similar situation before. It was due to the clashes.
You can use weblab viewer to rotate the side chain to fix the clashes.
Or try scwrl. In scwrl you can specify which residue's side chain you
want to change. 

-- 
Best regards,
 Qiang                            mailto:qiangl_at_uci.edu

=================Original message text===============
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   4.  RESULTS
-----------------------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST =    8193242
| TOTAL SIZE OF NONBOND LIST =    8193242

   NSTEP       ENERGY          RMS            GMAX         NAME   
NUMBER
      1       6.7439E+07     1.7942E+07     1.0385E+09     NZ       2889

 BOND    =      216.5081  ANGLE   =      905.7987  DIHED      =    
2173.1263
 VDWAALS = 67435606.3650  EEL     =    -4909.3228  HBOND      =       
0.0000
 1-4 VDW =     1417.0613  1-4 EEL =     3308.6923  RESTRAINT  =       
0.0000

****************************************

 Frac coord min, max:   0.0619183818  1.05405019
 The system has extended beyond 
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

****************************************

The vdwaals energy suggests some type of atomic clash, but the error
message about the virtual box suggests that there is a problem in the
size of the receptor.  Which one is it?

Thank you!

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