Hi Jason,
Thank you for your help! I have installed AmberTools 12 with amber11, but in the course of calculation with MMPBSA.py in AmberTools 12, the program can not work. The error message is:
PrmtopError: Prmtops must be either ALL chamber prmtops or NONE
Exiting. All files have been retained.
Using amber 11 and AmberTools 1.5 , the program can work normally. What is the problem with this in AmberTools 12? Thanks!
Best wishes
Yours sincerely
Duan Baogen
From: Jason Swails
Date: 2013-03-04 20:37
To: dbaogen; AMBER Mailing List
Subject: Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5
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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--
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 - 19:30:02 PST
