AMBER Archive (2009)

Subject: [AMBER] Antechamber and Parmchk problems

From: cyk5056 (
Date: Tue Nov 03 2009 - 20:22:38 CST

Hi everyone,
  I am using antechamber to prepare a prep file for a residue: TMS.pdb.
$AMBERHOME/exe/antechamber -i TMS.pdb -fi pdb -o TMS.prep -fo prepc -c bcc
  It works for my computer(call it Computer 1). However, when running using another's computer(Call it computer 2), It shows:
Total number of electrons: 198; net charge: 0
Running: /home/na3m/Download/AMBER10/amber10/bin/
Error: unable to find mopac charges in mopac.out

  For parmchk: I continue my work on Computer 1:
  $AMBERHOME/exe/parmchk -i TMS.prep -fi prepc -o TMS.frcmod
  It shows:
  Memory fault.
  I doubt it is the debugger's problem, so I copied TMS.prep and TMS.pdb to Computer 2 run the same parmchk instruction, it shows:
  Segmentation fault.
  I am puzzled about these problems. Seems they are similar however I do not know how to deal with them.
  PS: TMS.pdb and TMS.prep attached and both of the computer are using Amber10.

  Thank you very much!


  • application/octet-stream attachment: TMS.pdb

  • application/octet-stream attachment: TMS.prep

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