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.CE=,CD= | :TYR.CD=,CE= | :ASP.OD= | :GLU.OE= | :ARG.NH= | :ASN.ND2,OD1 :GLN.NE2,OE1 | :HIE.ND1,CD2,CE1,NE2 | :HID.ND1,CD2,CE1,NE2 | :HIP.ND1,CD2,CE1,NE2 | .H= | :150.O)",
<all in one line !!>
Thanks once again,
Cheers,
Sampath
--- On Mon, 3/9/09, David A. Case <case.biomaps.rutgers.edu> wrote:
> From: David A. Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Restraint Mask length restriction !!
> To: "AMBER Mailing List" <amber.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.CE=,CD= | :TYR.CD=,CE= | :ASP.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
>
>
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Received on Wed Mar 11 2009 - 01:11:10 PDT
