AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Mar 09 2009 - 14:50:08 CDT

Dear Sampath,

The limit on masks was indeed 80 characters in AMBER 9.

Bugfix 27 for AMBER 9 raises that limit to 256 characters:

http://ambermd.org/bugfixes/9.0/bugfix.27

********>Bugfix 27
Author: Ross Walker (posted by dac)
Date: 1/1/2007

Programs: Sander

Description: Complex masks for QM/MM can overflow the internal arrays
             in findmask(); also increase the mask string to 256 characters

Fix: apply the following patch to src/sander/findmask.f

Amber 10 supports masks up to 256 characters by default.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Sampath Koppole
> Sent: Monday, March 09, 2009 7:40 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Restraint Mask length restriction !!
>
>
> 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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