Hi all,
I installed AmberTools 12 resently and combine it with Amber11 by the following command:
export PATH=¡±$AMBERHOME/bin:/home/myname/amber11/bin:$PATH¡±
I ran entropy and decompsition calculation with MMPBSA.py.MPI ( or MMPBSA.py ) in AmberTools 12, but MMPBSA aborted with the error below:
Running MMPBSA.MPI on 12 processors
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/Amber/amber12/bin/cpptraj
mmpbsa_py_nabnmode found! Using /home/Amber/amber12/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
TrajError: Solvated topology 0 has IFBOX == 0
Error occured on rank 0.
Exiting. All files have been retained.
I am pretty sure that the prmtop files are nothing improper because when I submit the same task to AmberTools 1.5 , the job completes normally.
I installed AmberTools 12 in the following steps. Maybe this is something wrong with the installation.
tar jxvf AmberTools12.tar.bz2
export AMBERHOME=/home/Amber_I/amber12
cd /home/Amber_I/amber12
patch -p0 -N < bugfix.all ### from bugfix.1 to bugfix.7
./configure -nofftw3 gnu
make install
./configure -mpi gnu
make install
Here is my input file:
Per-residue GB and PB decomposition
&general
startframe=201, verbose=1,
strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
dec_verbose=1,
/
Anyone who can give me some suggestion about this error in AmberTools 12 ?
Many Thanks!
Cao Yang,
Zhejiang University
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Received on Thu May 31 2012 - 10:30:03 PDT
