AMBER Archive (2005)

Subject: Re: AMBER: pmemd and restraints

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Thu Jan 27 2005 - 03:01:31 CST

Dear all,
I had the same problemas Dr Lankas.
It seems that for pmemd from AMBER8 (as well as for sander I suppose),
the restraints have to be put under
the heating stuff, in contrary to what was done in sander from AMBER7.
I am not sur about that but when I placed restraint informations at the
end, pmemd did not complain.
However, there is a strange message in my mdout file, saying that no
restraint was defined, despite the fact that these restraints
have been read correctly before, and that RESTRAINT energy is not zero
during the simulation.
Here is the part of the mdout file with thses information :

   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
 Group input for protein restraints: 25 kcal/mol.

     GROUP 1 HAS HARMONIC CONSTRAINTS 25.00000
 GRP 1 RES 1 TO 442
      Number of atoms in this group = 6620
    ----- END OF GROUP READ -----

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 0 5000 100.000000 300.000000 0 0
 TEMP0 5001 25000 300.000000 300.000000 0 0

 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

Does anyone know what this last message is for ?
Thank you in advance,
Fabien

Filip Lankas wrote:

>
> 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.
> 25.0
> RES 1 24
> END
> END
> ***************************** md.in *****************************
> *************************************************************************
> Heating the system with 25 kcal/mol restraints on DNA, V=const
> &cntrl
> imin=0, ntx=1, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nscm=5000,
> ntf=2, ntc=2,
> ntb=1, ntp=0,
> nstlim=50000, t=0.0, dt=0.002,
> cut=9.0,
> tempi=100.0, ntt=1,
> ntr=1, nmropt=1,
> lastist=10000000
> &end
> 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: "md.in"
> Current format: 9208 FORMAT(20a4)
>
> Am I doing something wrong, or does pmemd simply not support this kind
> of task?
>
> Thank you in advance,
>
> Filip 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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