I've been trying to run MM/PBSA per-residue decomposition based on the
AMBER tutorial (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm) and
I'm having some problems. I've run explicit MD for my complex (n3_new ->
~800RES) and have created the "unsolvated"/implicit prmtop files
(n3_new_un.prmtop, N3_un.prmtop, and m3_un.prmtop) based upon the implicit
solvation AMBER tutorial (
http://ambermd.org/tutorials/basic/tutorial1/section4.htm), ultimately
creating the prmtop files from the 12Acut.
My mmpbsa.in script is as follows:
Per-residue GB and PB decomposition
&general
interval=1, verbose=2, keep_files=2,
/
&gb
igb=5, saltcon=0.150,
/
&pb
indi=1.0, exdi=80.0, istrng=0.15, fillratio=4.0,
/
&decomp
idecomp=2, dec_verbose=3
/
I've been running MM/PBSA in the command line and getting the following
error once the program processes the first .mdcrd file:
$ module load amber/12.0-intel
$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o final_results_mmpbsa.dat -do
final_decomp_mmpbsa.dat -sp n3_new.prmtop -cp n3_new_un.prmtop -rp
N3_un.prmtop -lp m3_un.prmtop -y *.mdcrd
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
sander found! Using /opt/crc/amber/amber12/intel/bin/sander
mmpbsa_py_energy found! Using /opt/crc/amber/amber12/intel/
bin/mmpbsa_py_energy
cpptraj found! Using /opt/crc/amber/amber12/intel/bin/cpptraj
Preparing trajectories for simulation...
*Error in box coord line of trajectory prod1.mdcrd.
Expect only 3 or 6 box coords.
Problem line: 10.694 53.454 38.966 11.951 54.257 39.225 5.906
Error: Could not set up prod1.mdcrd for reading.
Error: trajin: Could not set up trajectory.*
*TrajError: Trajectory prod1.mdcrd has 0 frames!
Exiting. All files have been retained.*
I used ptraj to look at the solvated mdcrd files and found that the
solvated complexes have converged, so I am not sure what exactly this error
message could mean and cannot find a precise answer online in the AMBER
threads. This error message suggests to me that the waterbox information is
missing from the solvated complex (n3_new.prmtop) file, yet it is not
missing.
I also get this same error message, just on other "problem lines" when I
run this same script on different systems. Do you have any insight on how I
can successfully run MM/PBSA per-residue decomposition or what I am doing
wrong?
Thank you.
--
Ashley Ferraro
aferrar1.nd.edu
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Received on Wed Jul 11 2012 - 17:30:04 PDT
