Problems when running FEP for mutation ASP to GLY

From: Yunhui Peng (yunhuip_at_g.clemson.edu)
Date: Fri Apr 17 2015 - 13:53:03 CDT

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Dear all,
   I am trying to run free energy perturbation calculation for mutation ASP
to GLY. The simulation always show the following mistakes:
FATAL ERROR: Bad global improper count!
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
[0] Stack Traceback:
  [0:0] LrtsAbort+0x51 [0xbcd8b1]
  [0:1] _Z8NAMD_bugPKc+0x77 [0x544157]
  [0:2] _ZN10Controller16compareChecksumsEii+0x355 [0x878275]
  [0:3] _ZN10Controller9integrateEv+0x1177 [0x86a1b7]
  [0:4] _ZN10Controller9threadRunEPS_+0x6b9 [0x87e879]
  [0:5] CthStartThread+0x1c [0xb254fc]
  [0:6] [0x3683e43900]

The page on the mutator plugin warns users about running alchemical FEP
calculations involving glycine (
http://www.ks.uiuc.edu/Research/vmd/plugins/mutator/)
. I also tried FEP calculation for ARG to GLY and it works fine. I don't
know why it doesn't work for ASP to GLY when I am using the same script. I
attach the the script used in the FEP calculation and hope someone can help
me with the problems
Thanks,
Yunhui

• application/octet-stream attachment: script.namd

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