The AmberTools 12 version of MMPBSA.py has the output designed to be in CSV
(comma-separated variable) format, which is different from the ASCII format
of Amber 11's MMPBSA.py. We did this so that the ouput file would be easier
to open and manipulate in your favorite spreadsheet program.
Unfortunately, MMPBSA.py only supports single alanine mutants and this
cannot currently be circumvented.
I hope that helps.
-Bill
On Wed, Sep 19, 2012 at 8:27 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg>wrote:
> Dear Amber users,
> I am currently familiarizing myself with the
> MMPBSA.py script using Amber12. I have couple of queries in this regard.
>
> FIRST:
>
> There is an issue with the decomposition calculation.
>
> My input script for the calculation is:
>
> ------------------------------------------------------------------
> &general
> startframe=1, endframe=10, interval=5,
> verbose=2, keep_files=2,
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &decomp
> idecomp=2, dec_verbose=0,
> print_res="191-204"
> /
> ---------------------------------------------------------------------
>
> In this case, The GB calculation went of fine, but There was nothing
> written on the decomp.out file and there is no specific error message.
>
> Then I tried by removing the "print_res" parameter. This time, there
> was an output written in the decomp.out file. But this looks very
> strange as shown below:
>
>
> -------------------------------------------------------------------------------
> Run on Wed Sep 19 15:50:46 2012
> idecomp = 2: Per-residue decomp adding 1-4 interactions to EEL and VDW.
> Energy Decomposition Analysis (All units kcal/mol): Generalized Born
> solvent
> D,E,L,T,A,S,:
> T,o,t,a,l, ,E,n,e,r,g,y, ,D,e,c,o,m,p,o,s,i,t,i,o,n,:
> Residue,Location,Internal,,,van der Waals,,,Electrostatic,,,Polar
> Solvation,,,Non-Polar Solv.,,,TOTAL,,
> ,,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of
> Mean,Avg.,Std. Dev.,Std. Err. of Mean,Avg.,Std. Dev.,Std. Err. of
> Mean,Avg.,Std. Dev.,Std. Err. of Mean
> ACE 1,R ACE
>
> 1,0.0,0.0,0.0,-0.0025,0.0005,0.000353553390593,-0.0125,0.0175,0.0123743686708,0.03,0.012,0.00848528137424,0.0,0.0,0.0,0.015,0.006,0.00424264068712
> PRO 2,R PRO
>
> 2,0.0,0.0,0.0,-0.0055,0.0015,0.00106066017178,-0.103,0.2,0.141421356237,0.1195,0.1985,0.140360696066,0.0,0.0,0.0,0.011,0.0,0.0
>
> -------------------------------------------------------------------------------
>
> I tried the same thing with AMBER11 and the calculations went of fine
> with and without the "print_res" parameter.
>
>
> -------------------------------------------------------------------------------
> | Run on Wed Sep 19 15:12:05 SGT 2012
> idecomp = 2: Decomposition per-residue adding 1-4 interactions added
> to EEL and VDW.
> Energy Decomposition Analysis (All units kcal/mol): Generalized Born
> solvent
>
> DELTAS:
> Total Energy Decomposition:
> Residue | Location | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. |
> TOTAL
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> LYS 191 | L LYS 2 | 0.000 +/- 3.488 | -1.467 +/- 0.704 |
> -51.570 +/- 1.970 | 52.261 +/- 1.819 | -0.173 +/- 0.016 |
> -0.949 +/- 4.455
> LYS 192 | L LYS 3 | 0.000 +/- 1.708 | -3.635 +/- 0.850 |
> -52.714 +/- 1.334 | 53.919 +/- 2.887 | -0.509 +/- 0.039 |
> -2.938 +/- 3.709
>
> --------------------------------------------------------------------------------
>
> So my question is, IS this an AMBER12 related issue or am I missing
> something? Will be glad to hear about it.
>
> SECOND:
>
> I am also trying to do the alanine scanning. I could run a test
> successfully with a single Alanine mutant. I was wandering if it is
> possible to run a double alanine mutant? I read in the mailing list
> that this is possible with MMPBSA.pl but not currently with MMPBSA.py.
> Is this is the case? Is there a way around doing this?
>
> Sorry for the long email.
>
> Will be glad if someone can give me an insight into these issues.
>
> Thank you,
> Dilraj.
>
>
>
>
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> 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 Wed Sep 19 2012 - 06:30:03 PDT
