Re: [AMBER] Problem in calculation per residue free energy decomposition

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 3 Mar 2015 08:53:42 -0500

On Tue, Mar 3, 2015 at 5:04 AM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:

> Dear Amber users,
> I am using MMPB/GB SA pymol to calculate free energy decompostion of the
> residues within the ligand bound to the receptor in a complex.
> I have used this input file for the calculations:
> Per-residue GB and PB decomposition
> |&general
> | endframe=5, verbose=1,
> | # entropy=1,
> |/
> |&pb
> | istrng=0.00,
> | inp=1,
> | radiopt=0
> |/
> |&decomp
> | csv_format = 1,
> | idecomp=1, print_res="615-660"
> | dec_verbose=1,
>
> and this command line to call for MMPBSA.py calculation:
>
> MMPBSA.py -O -i mmpbsa_2.in -o FINAL_RESULTS_MMPBSA.dat -do
> FINAL_DECOMP_MMPBSA.dat -sp all_sol_MMPBSA.top -cp all_nsol_MMPBSA.top -rp
> EGFR_MMPBSA.top -lp EGF_MMPBSA.top -y *.mdcrd
>

‚ÄčThe decomposition results are printed to the -do file
(FINAL_DECOMP_MMPBSA.dat). All you showed below was the
FINAL_RESULTS_MMPBSA.dat, which doesn't have any decomposition results in
it...

Did you look for the decomposition output file? Are the results in there?
Did the program end successfully?

If that output file does not exist, do the MMPBSA.py tests pass?

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 03 2015 - 06:00:03 PST
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