Seungyeul,
I used the following path:
MMPBSA=/share/apps/amber11/bin/MMPBSA
and it gave me an error:
/share/apps/amber11/bin/python2.6 /share/apps/amber11/bin/MMPBSA -O -i decomp_tb_nm.in -o decomp_tb.dat -sp ../tryp_bpti_1000.top -cp ../GENR/tryp_bpti_nw.top -rp ../tryp_nw.top -lp ../bpti_nw.top -y ../tryp_bpti_1000.trj -do decomp_tryp_bpti.dat
File "/share/apps/amber11/bin/MMPBSA", line 2
if [ -z $AMBERHOME ]; then
^
Do you understand it?
Thanks for your help,
Rami
On Aug 22, 2011, at 11:27 AM, Seungyeul Yoo wrote:
Hi Rami,
I think you should use the executable named "MMPBSA" not "MMPBSA.py" for serial node job.
For parallel, MMPBSA.MPI should be used.
MMPBSA called another executable in the path of $AMBERHOME/AmberTools/src/mmpbsa_py/.
I am not sure your problem is caused by this, but that is the right way to call the executables for MMPBSA calculations.
Best regards,
Seungyeul Yoo
On Aug 21, 2011, at 10:23 AM, Osman, Roman wrote:
Ray and MJ,
I am back from vacation and I wanted to report the same problem I had before (on a different system) with some additional information.
I want to describe briefly what is the setup:
I have conducted a 50 ns simulations of a complex between trypsin and bpti. with ptraj I extracted 10000 snapshots with 1000 waters around the protein after centering imaging and rms fitting. The trajectory is written without box information. I then wanted to use this to compute the interaction energy with MMPBSA_py. The input to my first attempt was:
&general
verbose=2, strip_mdcrd=1, strip_mask=":WAT",
entropy=0, startframe=1000, endframe=10000, interval=1000
/
&decomp
idecomp=2, dec_verbose=3,
/
&gb
igb=5, saltcon=0.150
/
&pb
istrng=0.150
/
stripping all the waters and sampling every 1000 frames for 10 snapshots.
the gb calculation works fine but the pb calculation works OK for the receptor but stops for the ligand and the complex with the following messages:
for the _MMPBSA_ligand_pb.mdout:
minimizing coord set # 7
PB Bomb in assignlvlset(): no atmsas 36 -1 20
38 1 22 -2
38 1 22 -2
38 1 22 -2
38 1 22 -2
38 1 22 -1
38 1 22 1
38 1 22 -2
PB Bomb in assignlvlset(): illegal insas flag 36 -1 20 -4
and for the _MMPBSA_complex_pb.mdout:
minimizing coord set # 7
PB Bomb in assignlvlset(): no atmsas 35 -1 35
37 1 37 -2
37 1 37 -2
37 1 37 -2
37 1 37 -2
37 1 37 -1
37 1 37 1
37 1 37 -2
PB Bomb in assignlvlset(): illegal insas flag 35 -1 35 -4
I don't know the meaning of these numbers so it was difficult to trace back to the origin of the error although it seemed to mee that it has to do with the assignment of the dielectric boundaries.
Since it seemed that the problem may be due to the coordinates of the ligand, I decided to determine at which point in the trajectory this happens by repeating the calculation with a finer interval. The input now is:
&general
verbose=2, strip_mdcrd=1, strip_mask=":WAT",
entropy=0, startframe=6600, endframe=7500, interval=10
/
&decomp
idecomp=2, dec_verbose=3,
/
&gb
igb=5, saltcon=0.150
/
&pb
istrng=0.150
/
As you can see it's al the same except the interval=10 and the range (startframe and endframe) brackets the #7 frame from the previous calculations.
To my surprise the entire calculation for the 91 frames finished normally.
The script I am using is as follows:
#!/bin/bash
#PBS -N MM_ALL
#PBS -j oe -V
#PBS -q serial_std
#PBS -l select=1:ncpus=1
#PBS -m e
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/intel/lib/intel64
cd $PBS_O_WORKDIR
MMPBSA=/share/apps/amber11/bin/MMPBSA.py
PYTHON="/share/apps/amber11/bin/python2.6"
SUB="$PYTHON $MMPBSA -O -i decomp_tb_nm.in -o decomp_tb.dat -sp ../tryp_bpti_1000.top -cp ../GENR/tryp_bpti_nw.top -rp ../tryp_nw.top -lp ../bpti_nw.top -y ./tryp_bpti_1000.trj -do decomp_tryp_bpti.dat"
echo $SUB
$SUB
Perhaps someone can disentangle this mystery.
Thanks for your help.
Rami
On Aug 2, 2011, at 12:08 PM, Ray Luo, Ph.D. wrote:
Let me first forward this to the mailing list for the sake of record keeping ...
Ray
---------- Forwarded message ----------
From: MengJuei Hsieh <mengjueh.uci.edu<mailto:mengjueh.uci.edu>>
Date: Tue, Aug 2, 2011 at 8:48 AM
Subject: Re: [AMBER] Problem with MMPBSA.py
To: "Ray Luo, Ph.D." <ray.luo.uci.edu<mailto:ray.luo.uci.edu>>, Roman Osman <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>>
Hi,
I got some error in normal mode on our linux server, but the PBSA
calculation did come through. So I suggest to checkout if PBSA/sander/nab
are updated and make sure that pbsa, leap, ptraj, nab, mmpbsa_py, and sander
are rebuilt after patches.
Also attached after the mail is the log I had with normal mode errors.
Best,
--
Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
From: "Ray Luo, Ph.D." <ray.luo.uci.edu<mailto:ray.luo.uci.edu>>
Date: Mon, 1 Aug 2011 17:48:04 -0700
To: Roman Osman <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>>
Rami,
MJ is running your job, it's slow ... but the patched code seems to be
working on Mac ... MJ is running it on Linux right now ...
----
MMPBSA -O -i decomp_lig.in -o decomp_lig.dat -sp ./cbp_ro
5_200_py.top -cp ./cbp_ro5_nw_py.top -rp ./cbp_3dwy_py.top -lp ./ro5_py.top
-y .
/cbp_ro5_200.trj -do cbp_ror3_decnw.dat
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/mjhsieh/amber11/bin/ptraj
sander found! Using /home/mjhsieh/amber11/bin/sander for GB calculations
sander found! Using /home/mjhsieh/amber11/bin/sander for PB calculations
nmode program found! Using /home/mjhsieh/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...100 frames were read in and
processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning nmode calculations with mmpbsa_py_nabnmode...
Calculating normal modes for 3 frames
calculating complex contribution for frame 0
calculating receptor contribution for frame 0
calculating ligand contribution for frame 0
calculating complex contribution for frame 1
calculating receptor contribution for frame 1
calculating ligand contribution for frame 1
calculating complex contribution for frame 2
calculating receptor contribution for frame 2
calculating ligand contribution for frame 2
Traceback (most recent call last):
File "/home/mjhsieh/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py", line
1343, in <module>
outfile.write(str(nmodenorm))
File "MMPBSA_mods/amberoutputs.py", line 2263, in __str__
File "MMPBSA_mods/amberoutputs.py", line 2302, in AvgStdev
File "MMPBSA_mods/amberoutputs.py", line 2319, in _tot_stdevs
IndexError: list index out of range
Roman Osman
roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
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_______________________________________________
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Roman Osman
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
Tel: 212-659-8627
Fax: 212-849-2456
e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
http://atlas.physbio.mssm.edu/~osmanlab
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Received on Mon Aug 22 2011 - 09:30:03 PDT
