[AMBER] bad atom type: cl error in MMPBSA decomp

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Fri, 12 Oct 2012 15:13:39 +0530

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
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
Exiting. All files have been retained.

MMPBSA input file
startframe=50, endframe=5000, interval=50,
verbose=2, keep_files=0,
igb=5, saltcon=0.150,
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
AMBER mailing list
Received on Fri Oct 12 2012 - 03:00:02 PDT
Custom Search