Hi all,
I'm using the python version of mmpbsa to estimate the entropic
contribution of the binding energy for a protein-dna complex. I
followed the tutorial posted in the amber website.
Any help is appreciated.
Khaled
Here is my input file:
Input file for running entropy calculations using NMode
&general
endframe=1000, keep_files=2,
/
&nmode
nmstartframe=1, nmendframe=1000,
nminterval=500,
/
and here is my output:
| nmstartframe=1, nmendframe=1000,
| nminterval=500,
|/|--------------------------------------------------------------
|Solvated complex topology file: ../../start.prmtop
|Complex topology file: ../../complex.prmtop
|Receptor topology file: ../../protein.prmtop
|Ligand topology file: ../../DNA.prmtop
|Initial mdcrd(s): ../run.mdcrd
|
|Best guess for receptor mask: ":1-195"
|Best guess for ligand mask: ":196-237"
|Calculations performed using 1000 frames.
|NMODE calculations performed using 2 frames.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature has been
multiplied in as 300 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
Complex:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
Receptor:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
Ligand:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: -1.0000 0.0000
Rotational: -1.0000 0.0000
Vibrational: -1.0000 0.0000
Total: -1.0000 0.0000
DELTA S total= 1.0000 +/- 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
Not all of your snapshots minimized within tolerable limits for nmode.
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Received on Tue Nov 09 2010 - 16:30:04 PST
