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.
-------------------------------------------------------------------------------
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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 £É modify the corresponding part in MMPBSA.py script? Thanks in advance!
Best wishes,
Yours Sincerely,
Duan Baogen
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Received on Mon Mar 04 2013 - 05:00:02 PST
