Hello,
My comments are below:
On Fri, Oct 29, 2010 at 10:46 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> I use this command:
>
> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
> This is the binding_energy.mmpbsa file:
> .GENERAL
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./com_vac.prmtop
> RECPT ./ricin.prmtop
> LIGPT ./antibody_vac.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
> #
> .PROGRAMS
>
Is there anything below this point in your input file? I'm simply
speculating here, but try taking .PROGRAMS out of your input file, since the
input parser may be looking for something in this section...
I do have 2 more suggestions: 1st -- if you have not yet applied the bug
fixes for amber10, I suggest you do so and recompile. 2nd -- Do the
mm_pbsa.pl tests work? If they do work, start with one of the input files
from the test cases and modify it until you get it to what you want. You
should be able to determine what exactly is breaking with your simulation,
or better yet, it may just work if your mistake is a trivial one that's
difficult to find.
Good luck!
Jason
>
>
> In mm_pbsa_readinput.pm, the line 76 is:
> print " Found $key => $value\n";
> Line 260 is:
> $r_pro->{$key} = $value; # Overwriting of entries allowed here since
> # default is set in &init_data()
>
>
>
>
>
> ________________________________
> From: Bill Miller III <brmilleriii.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, October 29, 2010 11:09:03 AM
> Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
>
> Can you show your input? And what is on lines 76 and 260 of
> mm_pbsa_readinput.pm?
>
> -Bill
>
> On Fri, Oct 29, 2010 at 10:50 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
>
> > Hello,
> > I use the binding_energy.mmpbsa from the tutorial A3 to calculate binding
> > energy. But I got these error messages:
> > Use of uninitialized value in concatenation (.) or string at
> > /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 76, <IN> line
> 59.
> > Use of uninitialized value in hash element at
> > /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 260, <IN> line
> > 59.
> > /usr/local/amber10/exe/sander -O -i pbsa_com.in -o pbsa_com.1.out
> > -c
> > ./snapshot_com.crd.1 -p ./com_vac.prmtop not successful
> >
> > I checked the mm_pbsa_readinput.pm, but don't know what I should do.
> > Could
> > anibody help me? Thank you.
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 29 2010 - 09:00:04 PDT
