AMBER Archive (2009)

Subject: Re: [AMBER] Restraint Mask length restriction !!

From: Sampath Koppole (sampathkoppole_at_yahoo.com)
Date: Mon Mar 09 2009 - 09:39:38 CDT

Dear Dr. Case,
Thanks once again.
The program stalls after

5. Reference Atom Coordinates.

I am pasting the last few lines of the output :

---------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
---------------------------------------------------------------------------

General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 1, ntb = 1, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 15.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Energy minimization:
     maxcyc = 5000, ncyc = 500, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 70.504 Box Y = 71.808 Box Z = 68.898
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 72 NFFT2 = 72 NFFT3 = 72
     Cutoff= 15.000 Tol =0.100E-04
     Ewald Coefficient = 0.17871
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES
--------------------------------------------------------------------------

After this the program crashes with:

> $MPI_HOME/bin/mpiexec -np $nproc $EXE -O -i mini.in -o output/mini.out -p $sys1.prmtop -c $sys1.inpcrd -x output/mini.mdcrd -r output/mini.rst -ref $sys1.inpcrd -inf output/mdinfo
Error in group input::atommask.f::atom_namelist
unknown symbol::
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
rank 0 in job 38 camm25_48496 caused collective abort of all ranks
  exit status of rank 0: killed by signal 9

So I guessed there is some problem with the my atom mask:
The full atom mask that I specify is as follows :

RESTRAINTMASK="(:2-23,33-150) & ! (:PHE_at_CE=,CD= | :TYR_at_CD=,CE= | :ASP_at_OD= | :GLU_at_OE= | :ARG_at_NH= | :ASN_at_ND2,OD1 :GLN_at_NE2,OE1 | :HIE_at_ND1,CD2,CE1,NE2 | :HID_at_ND1,CD2,CE1,NE2 | :HIP_at_ND1,CD2,CE1,NE2 | @H= | :150_at_O)",
<all in one line !!>

Thanks once again,
Cheers,
Sampath

--- On Mon, 3/9/09, David A. Case <case_at_biomaps.rutgers.edu> wrote:

> From: David A. Case <case_at_biomaps.rutgers.edu>
> Subject: Re: [AMBER] Restraint Mask length restriction !!
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Monday, March 9, 2009, 3:30 PM
> On Mon, Mar 09, 2009, Sampath Koppole wrote:
>
> >
> > In my mini.out file, the restrained mask (in bold) I
> see that is being processed is only the first 80 characters
> or so :
>
> > Here is the input file:
> >
> > Initial Structural Minimization with explicit water
> > &cntrl
> > imin=1, maxcyc=5000, ncyc=500, ntmin=1,
> > ntb=1, cut=15, ntpr=10, ntr=1,
> > RESTRAINT_WT=1.0,
> > RESTRAINTMASK="(:2-23,33-150) & !
> (:PHE_at_CE=,CD= | :TYR_at_CD=,CE= | :ASP_at_OD= | :
> > /
>
>
> This doesn't mean anything. The code snippet that
> copies the input file
> to the output only prints the first 80 characters (we
> should change
> this.) But the full line should still be available to the
> program. Do
> you have other evidence that your mask is not be processed
> correctly?
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

      

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