Dear community,
I've recently installed amber12 (composer XE 2013.1.117) and I'm
experiencing an error while running mmpbsa.py on a system where I've
previously run the very same calculation with amber11.
here follows the input:
GB/PBSA analysis
&general
startframe=1, endframe=1000, interval=20, verbose=2, keep_files=0,
strip_mask=:WAT,MG2,Na+,GTP,GDP,:1-438
/
&gb
igb=2, saltcon=0.150,
/
&pb
istrng=0.15, fillratio=4.0
/
I've launched mmpbsa.py trough the following command:
/usr/local/amber12/bin/MMPBSA.py -O -i mmpbsa_py.in -o MMPBSA_PB-GB.txt
-sp solvated_complex.top -cp complex.top -rp rec.top -lp lig.top -y
traj.mdcrd.bz2 >& mmpbsa_py.out
and this is the output:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/amber12/bin/cpptraj
Preparing trajectories for simulation...
ValueError: invalid literal for int() with base 10: 'an'
Exiting. All files have been retained.
I did a quick google search and I understood that it probably is a
python error, although I'm not experienced with python programming.
I also found something on amber mailing list,
http://archive.ambermd.org/201106/0285.html and related messages, but my
calculations are run on standard topologies generated by tleap found in
previous amber versions. Hereafter follows the head of each top
solvated_complex.top
%VERSION VERSION_STAMP = V0001.000 DATE = 06/21/12
14:17:25
%FLAG
TITLE
%
FORMAT(20a4)
%FLAG
POINTERS
%FORMAT(10I8)
254878 21 240786 14374 29476 19866 58636 45348 0
0
452886 77696 14374 19866 45348 86 194 85 55
1
0 0 0 0 0 0 0 1 119
0
0
complex.top
%VERSION VERSION_STAMP = V0001.000 DATE = 03/04/11
10:09:56
%FLAG
TITLE
%
FORMAT(20a4)
%FLAG
POINTERS
%
FORMAT(10I8)
13454 15 6623 6989 15021 9497 29072 21848 0
0
74154 865 6989 9497 21848 67 156 67 44
0
0 0 0 0 0 0 0 0 119
0
0
rec.top
%VERSION VERSION_STAMP = V0001.000 DATE = 03/02/11
11:56:55
%FLAG
TITLE
%
FORMAT(20a4)
%FLAG
POINTERS
%
FORMAT(10I8)
6742 14 3325 3495 7550 4746 14555 10953 0
0
37194 438 3495 4746 10953 43 99 50 29
0
0 0 0 0 0 0 0 0 26
0
0
lig.top
%VERSION VERSION_STAMP = V0001.000 DATE = 03/04/11
10:09:56
%FLAG
TITLE
%
FORMAT(20a4)
%FLAG
POINTERS
%
FORMAT(10I8)
6712 15 3298 3494 7471 4751 14517 10895 0
0
36960 427 3494 4751 10895 67 156 67 44
0
0 0 0 0 0 0 0 0 119
0
0
All test run (serial) from the amber test suite run successfully.
Any suggestion will be greatly appreciated.
Best regards,
Alessandro Contini
--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
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Received on Wed Jan 30 2013 - 04:00:02 PST
