some additional question regarding NMA in entropy calculations:
I've tried to increase speed of the entropy calculation using NMA
alterating RMSD threshold for the minimization and reduce number of its
cycles , (nmode_igb=1, drms=0.01, maxcyc=10). As the result I've obtained
empty output logs after mmgbsa for each test system. Does it means that NMA
have not been succeed?
James
| Run on Tue Oct 7 19:47:21 2014
|
|Input file:
|--------------------------------------------------------------
|&general
|startframe= 1, interval=20, keep_files=2,
strip_mask=:WAT:Cl-:NA+:K+:PPC, netcdf=1
|/
|&gb
|igb=5, saltcon=0.100,
|/
|&nmode
|nmstartframe=1, nminterval=1, nmode_igb=1, drms=0.01, maxcyc=10,
nmode_istrng=0.15,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Solvated complex topology file:
/data2/Gleb/script/Analysis/md_OR2W1-MULTI_Benzyl-acetate/protein.parm7
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s):
/data2/Gleb/script/Analysis/md_OR2W1-MULTI_Benzyl-acetate/md_go.nc
|
|Receptor mask: ":2-290"
|Ligand mask: ":1"
|Ligand residue name is "MOL"
|
|Calculations performed using 105 complex frames.
|NMODE calculations performed using 105 frames.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mol (Temperature is 298.15 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
2014-10-07 9:39 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> Dear Amber users!
>
> Performing mmgbsa with quasi-harmonic calculations for my receptor-agonist
> complex I've obtained very high free energy for typical "good" binder as
> the ligand. From the below results you can see that the main unfavorable
> contribution (=source of wrong free energy value) came from the enthropy
> term calculated here using quasi-harmonic method. Does it means that q-h
> calculations always produce bad results in comparison to NMA? Might the
> high enthopy be evedence of some problems with input data (e.g not
> convergence of the input trajectory)? Are there any imput options for Q-H
> which could improve results?
>
> 1)Enthalpy
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -27.3927 1.4357
> 0.1401
> EEL -5.2307 2.4454
> 0.2386
> EGB 10.8602 1.5605
> 0.1523
> ESURF -3.4942 0.1079
> 0.0105
>
> DELTA G gas -32.6234 2.7259
> 0.2660
> DELTA G solv 7.3660 1.5721
> 0.1534
>
> DELTA TOTAL -25.2574 2.2894
> 0.2234
>
>
> 2)ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
> Translational Rotational Vibrational Total
> Complex: 16.9767 17.7092 282.7339 317.4194
> Receptor: 16.9725 17.7089 282.4909 317.1720
> Ligand: 12.1949 8.8983 16.8228 37.9160
>
> DELTA S: -12.1908 -8.8980 -16.5798 -37.6686
>
> -------------------------------------------------------------------------------
>
> 3) Using Quasi-harmonic Entropy Approximation: DELTA G binding = 12.4112
>
>
> Thanks for help,
>
> James
>
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Received on Wed Oct 08 2014 - 02:00:02 PDT
