I believe you need to use AmberTools 12 for chamber support. It should
work with amber11, but you will need to add "search_path=1" to your input
file (to make sure that MMPBSA.py looks outside AMBERHOME, which would need
to be set to AmberTools 12).
As a note, you can remove use_sander=1. MMPBSA.py will use sander by
default with APBS or chamber topology files in AmberTools 12.
HTH,
Jason
On Mon, Mar 4, 2013 at 7:27 AM, dbaogen <dbaogen.gmail.com> wrote:
> Dear all,
>
> I try to calculate binding free energy using MMPBSA.py script
> with CHARMM force field in Amber software. The prmtop file is generated
> using "chamber" program in Amber. the input file for MMPBSA calculation is
> as following:
>
> &general
> startframe=1, endframe=1, interval=1,
> keep_files=1,strip_mdcrd=0,verbose=1,
> use_sander=1
> /
> &pb
> istrng=0.1,sander_apbs=1,
> /
> The program can be executed normally in the calculation part. But the
> problem is occurred in generation "FINAL_RESULTS_MMPBSA.dat " file.
> MMPBSA.py can not output the binding free energy data. The content of
> FINAL_RESULTS_MMPBSA.dat is:
>
> Run on Mon Mar 4 16:59:32 CST 2013
>
> |Input file:
> |--------------------------------------------------------------
> |MMPBSA input file for running GB
> |&general
> | startframe=1, endframe=1, interval=1,
> | keep_files=1,strip_mdcrd=0,verbose=1,
> | use_sander=1
> |/
> |&pb
> | istrng=0.1,sander_apbs=1,
> |/
> |--------------------------------------------------------------
> |Complex topology file: ./com.prmtop
> |Receptor topology file: ./rec.prmtop
> |Ligand topology file: ./lig.prmtop
> |Initial mdcrd(s): ./amber3508.crd
> |
> |Best guess for receptor mask: ":1-916"
> |Best guess for ligand mask: ":917-919"
>
> |Calculations performed using 1 frames.
> |Poisson Boltzmann calculations performed using iAPBS interface to sander
> (sander.APBS)
> |
> |All units are reported in kcal/mole.
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> Problem parsing PB output!
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> In the following, I checked the corresponding *.mdout files. IN these
> files, "UB = 1142.4543 IMP = 488.9334 CMAP = 0.0000 " energy
> term is only for CHARMM force field. Would you like to help me with this
> problem? whether should Ｉ modify the corresponding part in MMPBSA.py
> script? Thanks in advance!
>
> Best wishes,
> Yours Sincerely,
>
> Duan Baogen
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 04 2013 - 05:00:03 PST
