This is an error that has been seen several times before on the Amber list.
The problem is that the radius of flourine is not defined in the sander
source code. You can see a previous response to a similar error here:
http://archive.ambermd.org/201101/0220.html. Simply insert the parameters
for fluorine (atom type and radius) into the patch shown in that thread,
apply the patch, and recompile sander in serial and it should work for you
afterwards.
I hope that helps.
-Bill
On Fri, Oct 12, 2012 at 5:43 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Fri Oct 12 2012 - 05:30:03 PDT
