Dear all,
I am following the installation of MMPBSA.py as given in the TUTORIAL 3 of
AMBER ADVANCED TUTORIALS. We have amber10 installed. 1st step of tutorial
which involve installation and compilation of MMPBSA.py was successful as I
could see the MMPBSA.py file in “/opt/amber10/bin” directory. Here is the
output of command “make install”
/bin/bash setup.sh
Python version 2 detected. No file conversion necessary.
/bin/cp MMPBSA.py *pyc /opt/amber10/bin
The second step is checking of proper MMPBSA.py installation. Command “make
-f Makefile_at test.mmpbsa” returned following output.
cd mmpbsa_py && ./Run
This test will take awhile. Please be patient.
diffing mutant_complex.mdcrd.save with _MMPBSA_mutant_complex.mdcrd
PASSED
==============================================================
diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
==============================================================
To troublshoot I checked the file "mmpbsa.out". Following are the lines
contained in the file.
Warning: igb=5 should be used with either mbondi2 or bondi pbradii set.
Yours are modified Bondi radii (mbondi)
mdfil: Error unknown flag:
-y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
-radii radii]
Consult the manual for additional options.
.
.
.
mdfil: Error unknown flag:
-y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
-radii radii]
Consult the manual for additional options.
Error: Sander error! GB mdout file not created.
ptraj found! Using /opt/amber10/bin/ptraj
sander found! Using /opt/amber10/bin/sander (serial only!)
Checking mutant topology files...
Preparing trajectories with ptraj...
3 frames were read in and processed by ptraj for use in calculation.
Mutating complex mdcrd for alanine scanning...
Starting sander calls
Starting gb calculation...
Starting mutant gb calculation...
Starting pb calculation...
Starting mutant pb calculation...
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
..........................................................
While this is the part of file FINAL_RESULTS_MMPBSA.dat.dif
32,177d31
< GENERALIZED BORN:
< Complex:
< Energy Component Average Std. Dev. Std. Err. of
Mean
<
-------------------------------------------------------------------------------
< VDWAALS -2017.9409 7.6158
4.3970
< EEL -16941.2384 54.6141
31.5315
< EGB -3100.3169 7.4586
4.3062
< ESURF 96.5253 1.1714
0.6763
< TOTAL -10553.0038 35.2130
20.3302
< Receptor:
< Energy Component Average Std. Dev. Std. Err. of
Mean
<
-------------------------------------------------------------------------------
.
.
.
.
.<
-------------------------------------------------------------------------------
< VDWAALS -58.0643 4.3366
2.5037
< EEL -37.2044 2.2074
1.2744
< EPB 62.4453 2.9759
1.7181
< ECAVITY -4.8321 0.1006
0.0581
< DELTA G binding = -37.6555 +/- 1.5219
0.8787
< RESULT OF ALANINE SCANNING: (D231A MUTANT:) DELTA DELTA G binding =
0.2565 +/- 0.1727
<
-------------------------------------------------------------------------------
<
-------------------------------------------------------------------------------
< WARNINGS:
< igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are
modified Bondi radii (mbondi)
......................................................................
I could not figure out the meaning of "mdfil: Error unknown flag: -y" and
source of failure to run the test successfully. Kindly assist.
Cheers,
Ranajit Shinde
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Received on Wed Dec 30 2009 - 04:30:02 PST
