AMBER Archive (2009)

Subject: Re: [AMBER] PMEMD error message

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Mar 10 2009 - 10:39:38 CDT

Well, I see nmropt=1 without a comma behind it. I expect that the &wt
namelist should come before the group info too for ntr. I did not check out
the group info. These big blowups are very typical of namelist processing,
which for some compilers is less than totally friendly about the least
incorrect thing...
- Bob Duke
----- Original Message -----
From: "neville forlemu" <neville_forlemu_at_yahoo.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Tuesday, March 10, 2009 10:55 AM
Subject: [AMBER] PMEMD error message

hello,
I get this error message about my the following input file I modified from
the amber advanced tutorials 3 section 1 on MM-PBSA.

annealing solvated joxfact complex
&cntrl
imin=0,irest=0,ntx=1,
nstlim=50000,dt=0.002,
ntc=2,ntf=2,
cut=12.0,ntb=1,
ntpr=500,ntwx=500,
ntt=3,gamma_ln=2.0,
tempi=0.0,temp0=300.00,
ntr=1,
nmropt=1
/
500
res 1 50000
&wt TYPE='TEMP0',istep1=0,istep2=25000,
value1=0.1,value2=300.0,/
&wt TYPE='END'/

When I run the following command
mpirun -np 4 /opt/brinsoft/amber8/exe/pmemd -O -i heat.in -o heat.out -p
joxfact_wat.top -c joxfact_watmin.rst -r heat.rst -x heat.mdcrd -ref
joxfact_watmin.rst

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: "heat.in"
Current format: 9208 FORMAT(20a4)9018(/5x, 'GROUP', i5, ' HAS HARMONIC
CONSTRAINTS', f12.5)127(' ', 5x, '***PROBLEMS WITH GROUP ', a4, 14i5,
'*******', /)222(' ', 5x, 'Number of atoms in this group = ', i5)52(' ',
34x, i5, 2x, 'TO', i5)51(' ', 5x, 'GROUP', i5, 3x, 'CONSISTS OF ATOMS -',
/)46(' ', 5x, 'GROUP', i5, 3x, 'CONSISTS OF RESIDUE', i5, /)14(' GRP', i5, '
RES', i5, ' TO ', i5 )66(' ', 5x, '**** NUMBER OF FIND CARDS = ', i5, 2x,
'IS TOO BIG ******', /)202(' ', 5x, 'GRAPH NAME = ', a4, 2x, 'SYMBOL = ',
a2, 4x, 'TREE SYMBOL = ', a1, 5x, 'RESIDUE TYPE = ', a4, /)200(' ', 5x, 'ALL
ATOMS THAT MEET 1 OF THE FOLLOWING', ' SPECIFICATIONS WILL BE INCLUDED IN
GROUP BELOW', /)
^
IOT Trap
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 6

So I am wondering whether the size of my system (400000) could also be the
problem.
Need some help.
Thanks
Dadado

--- On Sun, 3/8/09, Ross Walker <ross_at_rosswalker.co.uk> wrote:
From: Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: [AMBER] PMEMD error message
To: "'AMBER Mailing List'" <amber_at_ambermd.org>
Date: Sunday, March 8, 2009, 4:52 PM

You are also missing a comma after nstlim=50000,dt=0.002

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Robert Duke
> Sent: Sunday, March 08, 2009 1:47 PM
> To: neville_forlemu_at_yahoo.com; AMBER Mailing List
> Subject: Re: [AMBER] PMEMD error message
>
> It's should be temp0, not tempO in the namelist (two places at least).
-
> Bob
> Duke
>
> ----- Original Message -----
> From: "neville forlemu" <neville_forlemu_at_yahoo.com>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Sunday, March 08, 2009 4:37 PM
> Subject: [AMBER] PMEMD error message
>
>
> Hello
>
> I get this error message, when I use the following command to heat up my
> system. It is complaining about a format error in my heat.in file. The
> file
> is shown below, has anyone had this problem and if yes what exactly in the
> file is it complaining. Thanks
>
>
> mpirun -np 4 /opt/brinsoft/amber8/exe/pmemd -O -i heat.in -o heat.out
> -p joxfact_wat.top -c joxfact_watmin.rst -r heat.rst -x heat.mdcrd -ref
> joxfact_watmin.rst
>
>
>
> lib-4324 : UNRECOVERABLE library error
>
>
>
>
>
> Encountered during a namelist READ from unit 5
>
> Fortran unit 5 is connected to a sequential formatted text file:
"heat.in"
>
> IOT Trap
>
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
>
> MPI: aborting job
>
> MPI: Received signal 6
>
>
>
>
> This is my heat.in file
> heating solvated joxfact complex
>
> &cntrl
>
> imin=0,irest=0,ntx=1,
>
> nstlim=50000,dt=0.002
>
> ntc=2,ntf=2,
>
> cut=12.0,ntb=1,
>
> ntpr=500,ntwx=500,
>
> ntt=3,gamma_ln=2.0,
>
> tempi=0.0,tempO=300.00,
>
> ntr=1,restraintmask=':1-50000',
>
> restraint_wt=2.0,
>
> nmropt=1
>
> /
>
> &wt TYPE='TEMPO',istep1=0,istep2=25000,
>
> value1=0.1,value2=300.0,/
>
> &wt TYPE='END'/
>
>
>
> Thanks
> Dadado
>
>
>
>
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