Thank You Very much for your response Carlos Simmerling and Jason. Sorry
for not providing my input and output files. Now i am providing that.*
*I am Looking at the stability calculation and want to see the pairwise
decomposition energy. I am using Amber11 with Amber tools 1.5.
*Input for run 1*
&general
startframe=1, endframe=1000, interval=10,
keep_files=1, netcdf=1,
/
&gb
igb=5, saltcon=0.1
/
&decomp
idecomp=3, dec_verbose=3,
/
*Input for Run 2:*
&general
startframe=1, endframe=1000, interval=10,
keep_files=1, netcdf=1,
/
&gb
igb=5, saltcon=0.1
/
&decomp
idecomp=4, dec_verbose=0,
/
Except the idecomp others are same. input trajectories, topologies are
same.
Output for idecomp=3: Pairwise decomposition adding 1-4 interactions added
to Internal.
Pairwise Energy Decomposition Analysis (All units kcal/mol): Generalized
Born solvent
Complex:
Total Energy Decomposition:
Resid 1 | Resid 2 | Internal | van der Waals |
Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
-----------------------------------------------------------------------------------------------------------------------------------------------------
PRO 1 | PRO 1 | 0.000 +/- 0.000 | -0.411 +/- 0.086 | -8.171
+/- 3.189 | -52.944 +/- 2.320 | 1.947 +/- 0.017 | -59.579 +/- 3.944
PRO 1 | GLN 2 | 0.000 +/- 0.000 | -0.859 +/- 0.176 | -22.013
+/- 1.614 | 0.313 +/- 1.000 | -0.314 +/- 0.021 | -22.873 +/- 1.907
PRO 1 | ILE 3 | 0.000 +/- 0.000 | -0.497 +/- 0.197 | -0.349
+/- 0.208 | 0.069 +/- 0.231 | -0.125 +/- 0.048 | -0.902 +/- 0.371
PRO 1 | THR 4 | 0.000 +/- 0.000 | -0.022 +/- 0.007 | -0.141
+/- 0.356 | 0.115 +/- 0.348 | 0.000 +/- 0.000 | -0.049 +/- 0.498
etc..
output for idecomp = 4: Pairwise decomposition adding 1-4 interactions
added to EEL and VDW.
Pairwise Energy Decomposition Analysis (All units kcal/mol): Generalized
Born solvent
Complex:
Total Energy Decomposition:
Resid 1 | Resid 2 | Internal | van der Waals |
Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
-----------------------------------------------------------------------------------------------------------------------------------------------------
PRO 1 | PRO 1 | 0.000 +/- 0.000 | 0.310 +/- 0.507 | 50.413
+/- 1.787 | -52.079 +/- 2.211 | 1.946 +/- 0.015 | 0.590 +/- 2.888
PRO 1 | GLN 2 | 0.000 +/- 0.000 | -0.450 +/- 0.274 | -8.293
+/- 1.360 | 0.426 +/- 1.120 | -0.306 +/- 0.021 | -8.623 +/- 1.783
PRO 1 | ILE 3 | 0.000 +/- 0.000 | -0.520 +/- 0.155 | -0.339
+/- 0.169 | 0.083 +/- 0.187 | -0.129 +/- 0.037 | -0.905 +/- 0.298
PRO 1 | THR 4 | 0.000 +/- 0.000 | -0.023 +/- 0.006 | -0.153
+/- 0.379 | 0.126 +/- 0.371 | 0.000 +/- 0.000 | -0.050 +/- 0.531
Jason sir, as u have mentioned "energy values between non-adjacent residues
for idecomp=3 and idecomp=4 are identical here. but why it is different for
adjacent residues and self (pro1 - pro 1)? shouldn't be the same too?
I want to see the contribution of each residue to the overall stability.
how should i go with my purpose? please suggest me please.
Once again Thank u for your reply.
Thank you
Rajeswari A
On Wed, Mar 14, 2012 at 7:04 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> On Wed, Mar 7, 2012 at 12:18 AM, Rajeswari A.
> <rajeswari.biotech.gmail.com>wrote:
>
> > Dear Amber users,
> >
> > As per the manual idecomp 3 - Pairwise decomp with 1-4 terms added to
> > internal potential terms
> > 4 - Pairwise decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW
> > potential terms.
> >
> > For my system when i did with idecomp 3 & 4 , in both cases, the internal
> > potential term was 0.000 +/- 0.000. and the total energy contribution of
> > the residues are different.
> >
>
> There are no pairwise internal potential terms, as far as I know. The
> interesting values are the pairwise non-bonded potentials (particularly
> VDW, EEL, and POL). Keep in mind that the POL energies are not pairwise
> decomposable due to the inclusion of all atoms in the calculation of the
> effective born radii, but it's a reasonable approximation. If you look at
> energy values between non-adjacent residues (that is, between residues that
> do not share a dihedral), the energy decompositions for idecomp=3 and
> idecomp=4 should be identical. If they are not, I think there may be a
> problem (note the caveat I mention below).
>
> What happens if you ignore all of the surface tension terms? I think there
> was a bug in gbsa=2 (that's been fixed recently -- I'll make a bugfix for
> Amber 11 shortly) that was giving rise to this type of behavior.
>
> 1. Is my calculation correct?
> > 2. which method of decomposition should i use?
> > 3. what is the reason for different total energy contribution of each
> > residue by different decomposition terms?
> >
>
> I do not understand exactly what you're seeing with #3. If you posted
> parts of the relevant output files that might help. I don't understand
> what is differing where, so it's hard to provide assistance.
>
> HTH,
> Jason
>
>
> >
> > Please Clarify my doubts.
> >
> > Thank you very much in advance
> >
> > Rajeswari A
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 15 2012 - 00:00:02 PDT
