AMBER Archive (2008)

Subject: RE: AMBER: regarding segfault during energy minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 30 2008 - 00:40:21 CDT

Hi Anamika,

 

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 7.3878E+08 5.4632E+07 2.1205E+10 O 50311

 BOND = 635.4719 ANGLE = 3767.4121 DIHED =
18625.3499
 VDWAALS = ************* EEL = -509956.6162 HBOND =
0.0000

 1-4 VDW = 8179.5683 1-4 EEL = 79691.9336 RESTRAINT =
0.0000

 

 

You have two atoms sitting on top of each other. Note the *'s for VDWaals
energy. This means the value is too big to fit in the space available in the
output file. Also note GMAX of 10^10 Kcal/mol/A2 on a single atom!. You
should take a careful look at your initial structure, particularly in the
region of the Oxygen atom 50311. You will need to fix this clash before you
can run the minimization.

 

Ross

 

 

/\

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|\oss Walker

 

| Assistant Research Professor |

| San Diego Supercomputer Center |

| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |

| http://www.rosswalker.co.uk | PGP Key available on request |

 

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