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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 19 2012 - 05:30:04 PDT
