AMBER: pmemd and restraints

From: Filip Lankas <>
Date: Wed, 26 Jan 2005 18:01:50 +0100

Hello Amber users,

I have a problem running pmemd with position restraints and increasing
temperature. The system is a piece of DNA with explicit ions and water,
periodic, PME. My input file looks like this:

Group input for DNA restraints: 25 kcal/mol.
RES 1 24
***************************** *****************************
Heating the system with 25 kcal/mol restraints on DNA, V=const
     imin=0, ntx=1, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
     ntf=2, ntc=2,
     ntb=1, ntp=0,
     nstlim=50000, t=0.0, dt=0.002,
     tempi=100.0, ntt=1,
     ntr=1, nmropt=1,
Heating from 100 to 300 K
  &wt type='TEMP0', istep1=0, istep2=5000, value1=100.0,
value2=300.0, &end
  &wt type='TEMP0', istep1=5001, istep2=50000, value1=300.0,
value2=300.0, &end
  &wt type='END', &end

.... the job starts, but crashes saying (in the stderr):

lib-4001 : UNRECOVERABLE library error
Encountered during a sequential formatted READ from unit 5
Fortran unit 5 is connected to a sequential formatted text file: ""
  Current format: 9208 FORMAT(20a4)

Am I doing something wrong, or does pmemd simply not support this kind
of task?

Thank you in advance,


Dr. Filip Lankas
Institute for Mathematics B
EPFL (Swiss Federal Institute of Technology)
Station 8
CH-1015 Lausanne
Tel: +41 21 693 2593    Fax: +41 21 693 5530
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Received on Wed Jan 26 2005 - 17:53:01 PST
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