If all of the tests pass, I would suggest taking the input file from the
test that is most similar to what you're trying to do (i.e. binding free
energy or something), and modifying the input file for your system.
Good luck!
Jason
On Fri, Jun 4, 2010 at 6:59 AM, <ANDREA.MEZGEZ.dicamp.units.it> wrote:
>
> Hello,
> I re-run the test:
> /amber11/test/make test.mm_pbsa
> with this conf in /amber11/src/mm_pbsa/Examples/Run.mmpbsa.test
> set clean &n bsp; &nb sp; = 1 ### REMOVE ALL FILES
> CREATED DURING THE TEST
> set do_01_GenerateSnapshots = 1 ### SNAPSHOTS SHOULD ALWAYS BE
> CREATED FOR SUBSEQUENT MM-PB/SA CALCULATIONS
> set do_02_MMPBSA_Stability = 1 ### SINGLE TRAJECTORY MM-PB/SA
> CALCULATION OF EFFECTIVE ENERGY
> set do_03_MMPBSA_Binding ; = 1 ### MM-PB/SA CALCULATION OF
> EFFECTIVE ENERGY OF BINDING
> set do_04_MMPBSA_NmodeNAB = 0 ### ENTROPY CALCULATION BY NMODE
> NORMAL MODE ANALYSIS USING NAB
> set do_05_MMPBSA_Decomp_Residue = 1 ### PER-RESIDUE DECOMPOSITION OF
> MM-PB/SA EFFECTIVE ENERGY OF BINDING
> set do_06_MMPBSA_Decomp_Pair = 0 ### PAIRWISE DECOMPOSITION OF
> MM-PB/SA EFFECTIVE ENERGY OF BINDING
> set do_07_MMPBSA_Hyb &nb sp; = 0 ### MM-PB/SA USING HYBRID
> SOLVATION METHOD
> set do_08_MMPBSA_Nmode & nbsp; = 0 ### ENTROPY CALCULATION BY
> NMODE NORMAL MODE ANALYSIS
> set do_09_MMPBSA_Nmode_Decomp = 0 ### DECOMPOSITION FOR NMODE
> set do_10_MMPBSA_Binding_Parallel = 0 ### PARALLEL EXECUTION OF BINDING
> CALCULATION
> and also try:
> /amber11/test/make make test.mmpbsa_py
> and all test passed!
> I'll try all test or big test?
> Bye,
> Andrea
> -----Original Message-----
> From: amber-bounces.ambermd.org on behalf of Jason Swails
> Sent: Thu 6/3/2010 6:03 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] mm_pbsa error on ambertools 1.4 amber11
> Hello,
> Did you run the test for mm_pbsa? Did those pass? (Note, try without
> your
> modification).
> All the best,
> Jason
> On Thu, Jun 3, 2010 at 11:39 AM, <ANDREA.MEZGEZ.dicamp.units.it> wrote:
> > Dear AMBER community!
> >
> > First: i'm a sys admin, not a power user of amber...
> >
> > Second: sorry for my english.
> >
> >
> >
> > The error we have is (ambertools 1.4, amber 11 both with patch on
> linux
> > centos 5.5 64bit system - 2 amd opteron 4 core, compiled with gnu and
> > openmpi):
> >
> >
> >
> > Use of uninitialized value in concatenation (.) or string at
> > /amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
> >
> > Use of uninitialized value in concatenation (.) or string at
> > /amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
> >
> > Use of uninitialized value in concatenation (.) or string at
> > /amber/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
> >
> > /amber/amber11/bin/sander -O -i pbsa_com.in -o pbsa_com.1.out
> -c
> > ./snapshot_com.crd.1 -p ./c_Q635A.prmtop not successful
> >
> > For details see:
> > [1]
> http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successf ul
> >
> This link doesn't work for me.
> >
> >
> >
> >
> >
> > If comment out the line:
> >
> >
> >
> > 596c596
> >
> > < print OUT " ipb = ${ipb}, inp = ${inp}, dielc
> =
> > ${dielc},\n";
> >
> > ---
> >
> > > #print OUT " ipb = ${ipb}, inp = ${inp},
> dielc =
> > ${dielc},\n";
> >
> >
> >
> >
> >
> > the program start but at the last step of the complex energy
> calculation
> > the output is freeze but the job still running.
> >
> >
> >
> > Thanks in advance,
> >
> > Andrea
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > [2]http://lists.amb ermd.org/mailman/listinfo/amber
> >
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> [3]http://lists.amb ermd.org/mailman/listinfo/amber
>
> References
>
> 1. 3D"http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_succes 2. 3D"
> http://lists.ambermd.org/mailman/listinfo/amber"
> 3. 3D"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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 04 2010 - 06:30:04 PDT
