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
Received on Fri Jun 04 2010 - 04:30:04 PDT
