Marawan,
You *should* not need to mention the ligand in order to get the
decomposition to work properly. Are you using the latest version of
MMPBSA.py that was released with AmberTools12? You should upgrade to this
version if you have not already. I will test this to see if I can reproduce
your observation on my local machine using AmberTools12, also.
Concerning your other questions...
1. You can use ifqnt regardless of the nature of your original trajectory.
If you want the ligand treated with QM then you will have to include it in
the QM mask. And this can be completed in parallel since MMPBSA.py simply
divides the frames evenly across frames.
2. The output is a comma separated value (CSV) file. You should be able to
open it in any spreadsheet program. There are a lot of decomposition
results, which can make it difficult to examine as a text file, which is
why we changed the format to CSV.
I hope that helps.
-Bill
On Tue, May 15, 2012 at 8:13 PM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Dear AMBER user,
>
> I'm doing a MMPBSA.py calculation on a ligand protein complex..The final
> file (FINAL_DECOMP_MMPBSA.dat) is empty. I have read similar problem but if
> my understanding was correct, it said that i need to mention the ligand as
> well in the print residue section. I have done so, i got the output this
> time, but i don't know why i should mention the ligand because the best
> guess mask has already mentioned the ligand correctly, here is my input:
>
>
> Input file for running PB and GB
> &general
> startframe=1, endframe=2, verbose=1, netcdf=1
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100, qm_residues="18-19"
> /
> &decomp
> idecomp=1, print_res="18-19" (this gives empty output, but
> print_res="320, 18-19" gives the results below )
> dec_verbose=1,
> /
>
> I have to other questions:
> 1-Can i use the ifqnt option eventhough my original trajectory is purely
> classical, i have read the manual and the AMBERtool but this was not
> clear...???.And if this is possible, do i need to include the ligand number
> as well or the script well correctly identify it to be included, and can
> this be paralleled or not....???
> 2-The output i got is messy, do i need a special program to open:
> | Run on Wed May 16 10:01:30 2012
> idecomp = 1: Per-residue decomp adding 1-4 interactions to Internal.
> 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
> LEU 18,R LEU
> 18,0.0,0.0,0.0,-2.115,0.32,0.22627416998,-0.048,0.237,0.167584307141,0.606,0.033,0.0233345237792,-0.2487312,0.0210168,0.0148611217988,-1.8057312,0.0710168,0.0502164608582
> GLY 19,R GLY
> 19,0.0,0.0,0.0,-0.2815,0.1265,0.0894490078201,0.1455,0.1245,0.0880347942577,-0.0415,0.0525,0.0371231060123,-0.0600228,0.0265788,0.0187940497158,-0.2375228,0.0810788,0.0573313692905
> MOL 320,L MOL
> 1,0.0,0.0,0.0,-32.6475,0.7305,0.516541503657,-6.953,0.136,0.0961665222414,18.4435,0.5875,0.415425233947,-5.1337764,0.0346572,0.0245063411369,-26.2907764,0.3136572,0.221789133088
>
> S,i,d,e,c,h,a,i,n, ,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
> LEU 18,R LEU
> 18,0.0,0.0,0.0,-1.6795,0.1775,0.125511453661,0.1155,0.0575,0.0406586399182,-0.1365,0.0455,0.032173358544,-0.2001996,0.0067716,0.00478824427948,-1.9006996,0.1962716,0.138784979314
> GLY 19,R GLY
> 19,0.0,0.0,0.0,-0.012,0.006,0.00424264068712,0.723,0.03,0.0212132034356,-0.612,0.038,0.0268700576851,-0.0552672,0.0218232,0.0154313327072,0.0437328,0.0521768,0.0368945691006
> MOL 320,L MOL
> 1,0.0,0.0,0.0,-32.6475,0.7305,0.516541503657,-6.953,0.136,0.0961665222414,18.4435,0.5875,0.415425233947,-5.1337764,0.0346572,0.0245063411369,-26.2907764,0.3136572,0.221789133088
>
> B,a,c,k,b,o,n,e, ,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
> LEU 18,R LEU
> 18,0.0,0.0,0.0,-0.436,0.143,0.10111626971,-0.163,0.295,0.20859650045,0.742,0.013,0.00919238815543,-0.0485388,0.0142524,0.0100779686882,0.0944612,0.1247476,0.0882098738967
> GLY 19,R GLY
> 19,0.0,0.0,0.0,-0.2695,0.1335,0.0943987552884,-0.578,0.095,0.0671751442127,0.571,0.091,0.064346717088,-0.0047556,0.0047556,0.00336271700861,-0.2812556,0.1342556,0.0949330451723
> MOL 320,L MOL
> 1,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
>
> Thanks in advance
> Marawan
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 15 2012 - 18:00:03 PDT
