Dear Amber community members,
I have performed MD simulation of protein-ligand complex with ligand
containing Cl atom.
While running MMPBSA decomposition analysis I got the following error.
Please suggest how can I correct this bad atom type error for Cl atom.
Do I need to give parameters for Cl atom? MMPBSA input file is given below.
-------
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
sander found! Using /home/gncp/Documents/MD/amber12/bin/sander
mmpbsa_py_energy found! Using
/home/gncp/Documents/MD/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/gncp/Documents/MD/amber12/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /home/gncp/Documents/MD/amber12/bin/sander
calculating complex contribution...
*bad atom type: cl*
CalcError: /home/gncp/Documents/MD/amber12/bin/sander failed with prmtop
2Q6S_BVT_VAC.prmtop!
Exiting. All files have been retained.
-----------
MMPBSA input file
-------
&general
startframe=50, endframe=5000, interval=50,
verbose=2, keep_files=0,
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=1, print_res="68; 43; 49; 53; 56; 58; 60-61; 74-76; 78; 82-83; 86;
120; 123-124; 133-137; 142; 147; 157-158; 269", dec_verbose=2
/
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 12 2012 - 03:00:02 PDT
