Hello Dwight,
The following is the command
mpirun -np $NPROCS /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/
mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
and the binding_energy.mmpbsa is
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./pdb1k4u_apo2.prmtop
RECPT ./1k4u.prmtop
LIGPT ./apocynin.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 0
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
could please check why i got that error.
Regards ,
Vani
On Tue, Apr 5, 2011 at 10:37 AM, Dwight McGee <dwight.mcgee.gmail.com>wrote:
> Hi,
>
> Can you provide the following information so that it can help us diagnose
> your problem. What did you specifically type on the command line to run
> this
> calculation (inputs/outputs if any)? Have you applied all bug fixes? Do you
> pass all the amber tests when you run *test_amber_parallel.sh?*
>
> On Mon, Apr 4, 2011 at 7:11 PM, vani panguluri <vanipanguluri.gmail.com
> >wrote:
>
> > Hello amber users,
> >
> > I am get the following error while executing mm_pbsa.pl.
> >
> > Exit code -5 signaled from qb504
> > Killing remote processes... At-entry must be first
> > For details see:
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > At-entry must be first For details see:
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > At-entry must be first For details see:
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > At-entry must be first For details see:
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > MPI process terminated unexpectedly
> > DONE
> > ------------------------------------------------------
> > Running PBS epilogue script - 04-Apr-2011 18:06:06
> > ------------------------------------------------------
> > Checking node qb504 (MS)
> > -> Killing process of vani: bash
> > -> Killing process of vani:
> > /home/packages/mvapich/1.1/intel-11.1/bin/mpispawn
> > -> Killing process of vani: [mm_pbsa.pl]
> > /usr/local/sbin/node_cleaner: line 86: kill: (3307) - No such process
> > -> Killing process of vani: [mm_pbsa.pl]
> > /usr/local/sbin/node_cleaner: line 86: kill: (3308) - No such process->
> > Killing process of vani: [mm_pbsa.pl]
> > /usr/local/sbin/node_cleaner: line 86: kill: (3309) - No such process
> > -> Killing process of vani: [mm_pbsa.pl]/usr/local/sbin/node_cleaner:
> line
> > 86: kill: (3310) - No such process
> > -> Killing process of vani: [mm_pbsa.pl]
> > /usr/local/sbin/node_cleaner: line 86: kill: (3311) - No such process->
> > Killing process of vani: [mm_pbsa.pl]
> > /usr/local/sbin/node_cleaner: line 86: kill: (3313) - No such process
> > -> Killing process of vani: [mm_pbsa.pl]/usr/local/sbin/node_cleaner:
> line
> > 86: kill: (3314) - No such process
> > Checking node qb504 ok
> >
> >
> > can anyone help me to solve this error.
> >
> > Regards,
> > Vani
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 05 2011 - 11:30:03 PDT
