Dear Amber community members,
I have 100ns MD trajectories for a protein-ligand complex with around 276
residues.
I have submitted the following job for MMPBSA and decomposition analysis.
Only 3 frames were included in this trial job with 8 AAs for which decomp
analysis was requested.
The GB analysis is finished quickly but decomposition analysis is running
for more than three days.
How can I monitor the status of the job? when it is likely to finish? Is
there something wrong in the input structure/command? Will running the job
in parallel help?
I have used the following command.
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa_decomp.in -o results_decomp.dat -do
FINAL_DECOMP_MMPBSA.dat -cp complex_VAC.prmtop -rp protein.prmtop -lp
lig.prmtop -y 100ns_VAC.mdcrd
I'm using a Opensuse 12.01 system with 4GB ram and 1 cpu.
Input file: mmpbsa_decomp.in
---------
Sample input file for GB and decomp calculation
&general
startframe=50, endframe=5000, interval=2000,
verbose=2, keep_files=0,
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=2, print_res="267; 117; 243; 68; 83; 79; 80; 82", dec_verbose=3
/
Thank you.
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Wed Aug 15 2012 - 23:00:05 PDT
