AMBER Archive (2009)

Subject: Re: [AMBER] Using idecomp=3 with igb=10 (PB)

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Mon Oct 12 2009 - 14:51:23 CDT

Hi Chris,

First of all one has to be aware of that all these decomposition schemes are artificial and from a strictly physical point of view not correct.
Formally they are possible to perform since the applied force field is composed as a sum of second order (bond length terms, coulomb, vdw, gb), third order (bond angle term, surface area) and fourth order (torsion angle terms) interactions.
On the other hand, there are a couple of studies that show significant correlations between predicted decompositions on a per-residue level and the effects of experimental point mutations.

To summarize:
If you are interested in the total effect of a point mutation or if you want to predict binding hot spots, the decomposition on the per-residue level is the method of choice.
If you want to gain insights into which direct interactions for example a ligand makes to the residues of its binding interface, the pairwise per-residue decomposition helps you.

In my opinion the per-residue decomposition is in most cases more useful since it can more directly be compared to experimental observations. Also, if you want to predict binding hot spots, the total contribution of a residue decides whether it favours or disfavours the complex state.

I hope that resolves a little bit your confusion.

Hannes

-------- Original-Nachricht --------
> Datum: Mon, 12 Oct 2009 16:56:06 +0100
> Von: Chris Whittleston <csw34_at_cam.ac.uk>
> An: AMBER Mailing List <amber_at_ambermd.org>
> Betreff: Re: [AMBER] Using idecomp=3 with igb=10 (PB)

> Hey Hannes,
>
> I think I must be confused about what idecomp=1 is doing...
>
> To clarify - I just want to look at the interaction between each residue
> of
> a protein (one at a time) and a ligand e.g.
>
> 1 -> ligand
> 2 -> ligand
> 3 -> ligand
> ...etc
>
> So - this gives me information for a specific binding mode, which
> interaction are energetically most 'important'. I'm not interested in the
> interaction of the residue with it's neighbors, or its internal/self
> interaction energy.
>
> Up to now, I have been using idecomp=3 with the GB solvent representation
> as
> it is quick. This gives me more information than I need (1->2, 1->3 etc),
> so
> I just extract the interaction of each residue with the ligand from the
> total output. As far as I know, this is completely valid for studying what
> I
> specified above. The problem with using PB (apart from you can't decompose
> it in AMBER9!), is that as you pointed out, each calculation required
> solving the PB equation again - a costly process. It was suggested by
> various people on this list that using idecomp=1 would be a better option,
> as you can specify which interactions you want to look at. But, from what
> you say in your previous email, I cannot actually look just at the
> interactions of residue 1-> ligand, and then 2->ligand using idecomp=1
> without including 1<->1 or 2<->2 - correct? It just seems a bit odd to me
> that the self terms are included even though we are specifying ligand and
> receptor (LRES and RRES) in the input as two seperate entities - so we are
> clearly interested only in the interaction between them.
>
> Chris
>
> 2009/10/11 Hannes Kopitz <Hannes.Kopitz_at_gmx.de>
>
> > Hia Chris,
> >
> > If you want to check the per-residue decomposition against the pairwise
> > per-residue decomposition for a certain residue, you need to sum up all
> > pairwise interactions of this residue to all residues (including
> itself).
> > I'm not really sure what your intention was, but you can't expect in
> your
> > example below when you set "RRES 159 159" and "LRES 230 230" together
> with
> > idecomp=1 to obtain the pairwise contribution of the interaction between
> 159
> > and 330. What you actually get in this case when looking at the per
> residue
> > contribution of 159 for example is the sum of 159<->159 and 159<->330
> which
> > also contains (in my opinion) a contribution of the internal self energy
> of
> > 159 which is the reason for "int" not being zero.
> >
> > So if you like to check the per-residue decomposition against the
> pairwise
> > per-residue decomposition, my recommendation is: (1) Don't omit any
> residue
> > in the RRES and LRES cards. (2) Sum up all pairwise contributions
> > (idecomp=3) of a residue of interest (including its self contribution)
> and
> > compare this sum to the per-residue contribution (idecomp=1) of this
> > residue.
> >
> > Good luck!
> > Hannes
> >
> >
> > -------- Original-Nachricht --------
> > > Datum: Fri, 9 Oct 2009 16:16:53 +0100
> > > Von: Chris Whittleston <csw34_at_cam.ac.uk>
> > > An: AMBER Mailing List <amber_at_ambermd.org>
> > > Betreff: Re: [AMBER] Using idecomp=3 with igb=10 (PB)
> >
> > > Dear Hannes,
> > >
> > > Thanks for the reply! Firstly, I'm aware that igb was set to 1 - I
> > thought
> > > it was best to test this using the significantly faster GB calculation
> > and
> > > then simply change to igb=10 once I was convinced I had the same
> result
> > > coming from both idecomp settings. Thanks for the pointer about the
> > mmpbsa
> > > script - I have a collegue using it at the moment and so I will make
> sure
> > > I
> > > take all the PB settings from there when I do make the switch to
> igb=10.
> > I
> > > have modified my input files as you suggested to include all receptor
> and
> > > ligand residues for both types of decomposition here as I'm using GB
> > which
> > > is fast. I have also tested setting RRES 159 159 and the output for
> > > residue
> > > 159 does not change for idecomp=3 so that's ok. Here are the new input
> > > files, they are identical apart from idecomp=1 or 3:
> > >
> > > idecomp=1
> > > input file:
> > >
> > > Interaction energy per residue input for SANDER
> > > &cntrl
> > > imin = 1,
> > > idecomp = 1,
> > > ncyc = 1,
> > > maxcyc = 0,
> > > igb = 1, saltcon=0.1,
> > > ntb = 0,
> > > cut = 999.0,
> > > rgbmax = 8.22,
> > > /
> > > Protein
> > > RRES 1 329
> > > END
> > > Ligand
> > > LRES 330 330
> > > END
> > > Printing
> > > RES 1 330
> > > END
> > > END
> > >
> > > output sample for residue 159:
> > >
> > > ...
> > > TDC 158 55.995 -7.484 -62.004 -4.598 0.000
> > > TDC 159 -191.255 -10.122 45.124 -13.057 0.000
> > > TDC 160 53.978 -10.247 -68.584 -0.868 0.000
> > > ...
> > >
> > > idecomp=3
> > > input file:
> > >
> > > Interaction energy per residue input for SANDER
> > > &cntrl
> > > imin = 1,
> > > idecomp = 3,
> > > ncyc = 1,
> > > maxcyc = 0,
> > > igb = 1, saltcon=0.1,
> > > ntb = 0,
> > > cut = 999.0,
> > > rgbmax = 8.22,
> > > /
> > > Protein
> > > RRES 1 329
> > > END
> > > Ligand
> > > LRES 330 330
> > > END
> > > Printing
> > > RES 1 330
> > > END
> > > END
> > >
> > > output sample for residue 159:
> > > ...
> > > TDC 159-> 329 0.000 0.000 -2.300 2.299 0.000
> > > TDC 159-> 330 0.000 -1.146 -25.181 19.673 0.000
> > > TDC 160-> 1 0.000 0.000 -0.001 0.001 0.000
> > > ...
> > > As I mentioned above, setting RRES -> RRES 159 159 gives identical
> output
> > > for this residue.
> > >
> > > So - as you can see, the interaction energy from 159 -> 330 comes out
> > > significantly differently for idecomp=3 and idecomp=1. This is still
> > > puzzling me a lot as I cannot imagine why it should looking at just
> the
> > > interaction between residue 159 and 330. I'm also confused as to why
> > there
> > > is an internal energy in the first place as these residues (1-329 and
> > 330)
> > > are not covelently linked, so there should not be any 'internal
> > > interaction
> > > energy'. For idecomp=3, int is always 0.000 which makes a lot more
> sense
> > > to
> > > me.
> > >
> > > Thanks a lot for the help, it is much appriciated :)
> > >
> > > Chris
> > >
> > > 2009/10/8 Hannes Kopitz <Hannes.Kopitz_at_gmx.de>
> > >
> > > > Dear Chris,
> > > >
> > > > Sorry for my delayed comment on this!
> > > >
> > > > First of all, in the example below you set igb=1 whis is GB not PB.
> > > > If you want to use PB you should set igb=10 together with dbfopt=1
> and
> > > > istrng instead of saltcon and some more PB specific parameters.
> > > Regarding
> > > > this I strongly recommend you to read chapter 3.2 of the AMBER10
> > manual.
> > > A
> > > > more simple and I think also more secure way it would be to use the
> > > mm_pbsa
> > > > perl scripts for this.
> > > >
> > > > Now to the apparently confusing differences you obtained:
> > > >
> > > > If you want to perform a per residue decomposition you always need
> to
> > > set
> > > > the RRES card to all residues of the receptor and the LRES card to
> all
> > > > residues of the ligand. If you omit any residues here, you would
> obtain
> > > > incomplete per residue contributions lacking the terms of the
> pairwise
> > > > contributions to the omitted residues. This is at least true for the
> GB
> > > > term. For the PB term you would obtain the whole per residue
> > > contribution
> > > > also in the case you omit any residues in the RRES and LRES cards.
> But
> > > I'm
> > > > not sure how this behaves with respect to all other contributions
> (int,
> > > eel,
> > > > vdw, ...).
> > > > So in the case of any per residue decomposition my recommendation is
> to
> > > set
> > > > the RRES and LRES cards to all of the receptor and ligand residues
> > > > respectively, and to set the RES card to the fraction of residues
> you
> > > are
> > > > interested in.
> > > >
> > > > This is different in the case of a pairwise per residue
> decomposition.
> > > Here
> > > > you can set the RRES and LRES cards only to the fractions of
> residues
> > > you
> > > > are interested in. And this is strongly recommended for a pairwise
> PB
> > > > decomposition since here the PB equation has to be solved N-times,
> with
> > > N
> > > > being the number of residues included in the RRES and LRES card.
> > > >
> > > > I think this problem is actually a mistake of the manual since it
> > > doesn't
> > > > point this out. We need to change this in the future.
> > > >
> > > > I hope this helps you.
> > > >
> > > > Cheers!
> > > > Hannes
> > > >
> > > > -------- Original-Nachricht --------
> > > > > Datum: Thu, 8 Oct 2009 11:47:22 +0100
> > > > > Von: Chris Whittleston <csw34_at_cam.ac.uk>
> > > > > An: AMBER Mailing List <amber_at_ambermd.org>
> > > > > Betreff: Re: [AMBER] Using idecomp=3 with igb=10 (PB)
> > > >
> > > > > Just to clarify - as the pairwise per-residue (idecomp=3)
> > > decomposition
> > > > > does
> > > > > not give an internal energy, I have not been including it when
> > looking
> > > at
> > > > > the idecomp=1 values.
> > > > >
> > > > > Chris
> > > > >
> > > > > 2009/10/7 Chris Whittleston <csw34_at_cam.ac.uk>
> > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > Thanks for all your help on this already - I have just returned
> to
> > > this
> > > > > > problem now that I have an AMBER10 license, and am still having
> > > trouble
> > > > > > understanding the group specification. I have decomposed the
> energy
> > > two
> > > > > > ways, using idecomp=1 and idecomp=3 just to make sure they give
> the
> > > > same
> > > > > > answer when I look at a single residue, in this case 159. The
> > > protein
> > > > > runs
> > > > > > from residue 1->329 and the ligand is residue 330.
> > > > > >
> > > > > > Here is my idecomp=3 SANDER input file:
> > > > > >
> > > > > > Interaction energy per residue input for SANDER
> > > > > > &cntrl
> > > > > > imin = 1,
> > > > > > idecomp = 3,
> > > > > > ncyc = 1,
> > > > > > maxcyc = 0,
> > > > > > igb = 1, saltcon=0.1,
> > > > > > ntb = 0,
> > > > > > cut = 999.0,
> > > > > > rgbmax = 8.22,
> > > > > > /
> > > > > > Protein
> > > > > > RRES 1 329
> > > > > > END
> > > > > > Ligand
> > > > > > LRES 330 330
> > > > > > END
> > > > > > Printing
> > > > > > RES 1 330
> > > > > > END
> > > > > > END
> > > > > >
> > > > > > As expected, this gives a pairwise per-residue decomposition -
> so
> > to
> > > > > look
> > > > > > for interactions to residue 330, I just use:
> > > > > >
> > > > > > grep TDC sander.out | grep '\-> 330'
> > > > > >
> > > > > > Here is a sample of the output from grep:
> > > > > > ...
> > > > > > TDC 157-> 330 0.000 -0.061 0.892 -0.839
> > > 0.000
> > > > > > TDC 158-> 330 0.000 -0.024 -0.100 0.091
> > > 0.000
> > > > > > TDC 159-> 330 0.000 -1.146 -25.181 19.673
> > > 0.000
> > > > > > TDC 160-> 330 0.000 -1.158 -0.396 0.434
> > > 0.000
> > > > > > TDC 161-> 330 0.000 -0.087 -0.020 0.037
> > > 0.000
> > > > > > TDC 162-> 330 0.000 -0.008 0.218 -0.216
> > > 0.000
> > > > > > ...
> > > > > >
> > > > > > So - adding up the interaction energy from 159->330, you get
> > > > > -6.654kcal/mol
> > > > > >
> > > > > > Now - as Hannes pointed out, I really want to be using
> idecomp=1,
> > > > > > especially when using PB as I waste a lot of time calculating
> > > > > interactions I
> > > > > > just throw away. Unfortunately, so far I have been unable to
> > > reproduce
> > > > > this
> > > > > > value for residue 159. Here is the idecomp=1 input I'm using to
> > test
> > > > > this:
> > > > > >
> > > > > > Interaction energy per residue input for SANDER
> > > > > > &cntrl
> > > > > > imin = 1,
> > > > > > idecomp = 1,
> > > > > > ncyc = 1,
> > > > > > maxcyc = 0,
> > > > > > igb = 1, saltcon=0.1,
> > > > > > ntb = 0,
> > > > > > cut = 999.0,
> > > > > > rgbmax = 8.22,
> > > > > > /
> > > > > > Protein
> > > > > > RRES 159 159
> > > > > > END
> > > > > > Ligand
> > > > > > LRES 330 330
> > > > > > END
> > > > > > Printing
> > > > > > RES 159
> > > > > > END
> > > > > > END
> > > > > >
> > > > > > Here, I'm only printing for residue 159 and I get:
> > > > > >
> > > > > > PRINT DECOMP - TOTAL ENERGIES
> > > > > >
> > > > > > resid |internal |vdw |eel |pol |sas
> > > > > > ============================================================
> > > > > > TDC 159 -238.487 -2.889 130.226 -35.665 0.000
> > > > > >
> > > > > > This is clearly a different total interaction! What am I missing
> > > here?
> > > > > Is
> > > > > > it something to do with how you specify groups as I've tried all
> > > sorts
> > > > > of
> > > > > > things (switching LRES<->RRES, LRES and RRES ->RES etc) and
> nothing
> > > can
> > > > > > produce that same total interaction between residue 159 and 330.
> > > > > >
> > > > > > What is causing this difference?
> > > > > >
> > > > > > Any help figuring this out is much appriciated!
> > > > > >
> > > > > > Chris
> > > > > >
> > > > > >
> > > > > > 2009/7/28 Ashish Runthala <ashish.runthala_at_gmail.com>
> > > > > >
> > > > > > Hello Chris,
> > > > > >>
> > > > > >> See this output, you will realize what is the problem out
> there.
> > > > > >>
> > > > > >>
> > > > > >> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> =
> > > > > 0.0
> > > > > >> Etot = ************ EKtot = 0.0000 EPtot =
> > > > > ************
> > > > > >> BOND = 27342.0949 ANGLE = 978.1773 DIHED =
> > > > > 1354.4338
> > > > > >> 1-4 NB = 5277.1875 1-4 EEL = 7145.0848 VDWAALS =
> > > > > ************
> > > > > >> EELEC = -9360.5582 EHBOND = 0.0000 RESTRAINT =
> > > > > 0.0000
> > > > > >>
> > > > > >>
> > > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > > > >>
> > > > > >> vlimit exceeded for step 0; vmax = 24186095.7
> > > > > >>
> > > > > >> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS
> =
> > > > > 0.0
> > > > > >> Etot = ************ EKtot = 0.0000 EPtot =
> > > > > ************
> > > > > >> BOND = 27342.0949 ANGLE = 978.1773 DIHED =
> > > > > 1354.4338
> > > > > >> 1-4 NB = 5277.1875 1-4 EEL = 7145.0848 VDWAALS =
> > > > > ************
> > > > > >> EELEC = -9360.5582 EHBOND = 0.0000 RESTRAINT =
> > > > > 0.0000
> > > > > >>
> > > > > >>
> > > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > > > >>
> > > > > >>
> > > > > >> A V E R A G E S O V E R 1 S T E P S
> > > > > >>
> > > > > >>
> > > > > >> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS
> =
> > > > > 0.0
> > > > > >> Etot = ************ EKtot = 0.0000 EPtot =
> > > > > ************
> > > > > >> BOND = 27342.0949 ANGLE = 978.1773 DIHED =
> > > > > 1354.4338
> > > > > >> 1-4 NB = 5277.1875 1-4 EEL = 7145.0848 VDWAALS =
> > > > > ************
> > > > > >> EELEC = -9360.5582 EHBOND = 0.0000 RESTRAINT =
> > > > > 0.0000
> > > > > >>
> > > > > >>
> > > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > > > >>
> > > > > >>
> > > > > >> R M S F L U C T U A T I O N S
> > > > > >>
> > > > > >>
> > > > > >> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS
> =
> > > > > 0.0
> > > > > >> Etot = 0.0000 EKtot = 0.0000 EPtot =
> > > > > 0.0000
> > > > > >> BOND = 0.0002 ANGLE = 0.0000 DIHED =
> > > > > 0.0000
> > > > > >> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> > > > > 0.0000
> > > > > >> EELEC = 0.0001 EHBOND = 0.0000 RESTRAINT =
> > > > > 0.0000
> > > > > >>
> > > > > >>
> > > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > > > >>
> > > > > >> Total Energy is coming very high. So this system is totally
> > > unstable.
> > > > > >> You do one thing. This i checked to check the confirmation.
> > > > > >>
> > > > > >> You do one thing.Try minimizing the energy of the system. And
> then
> > > > > >> work your script out. Make the system with stable with lowest
> > > feasible
> > > > > >> energy.
> > > > > >> Ashish
> > > > > >>
> > > > > >>
> > > > > >> On Tue, Jul 28, 2009 at 6:17 PM, Hannes
> > > Kopitz<Hannes.Kopitz_at_gmx.de>
> > > > > >> wrote:
> > > > > >> > Hi Chris,
> > > > > >> >
> > > > > >> > Sorry, my mistake. It should be something like ...
> > > > > >> >
> > > > > >> > ...
> > > > > >> > RRES 1 318
> > > > > >> > END
> > > > > >> > LRES 319 319
> > > > > >> > END
> > > > > >> > RES 1 319
> > > > > >> > END
> > > > > >> > END
> > > > > >> >
> > > > > >> > The RRES and LRES cards define the residues to be considered
> for
> > > > > >> decomposition, whereas the RES card defines the residues for
> the
> > > > > output.
> > > > > >> > Moreover you should chose idecomp=1 for a per-residue
> > > decomposition.
> > > > > >> With idecomp=3 you would get a pairwise per-residue
> decomposition.
> > > > > >> > Also set ntmin to 2 and maxcyc to 0, cause you don't really
> want
> > > to
> > > > > >> perform any minimization step.
> > > > > >> > But anyway, for doing a PB decomposition you need AMBR10.
> > > > > >> > I hope that helps.
> > > > > >> >
> > > > > >> > Cheers!
> > > > > >> > Hannes
> > > > > >> >
> > > > > >> > -------- Original-Nachricht --------
> > > > > >> >> Datum: Tue, 28 Jul 2009 11:54:09 +0100
> > > > > >> >> Von: Chris Whittleston <csw34_at_cam.ac.uk>
> > > > > >> >> An: AMBER Mailing List <amber_at_ambermd.org>
> > > > > >> >> Betreff: Re: [AMBER] Using idecomp=3 with igb=10 (PB)
> > > > > >> >
> > > > > >> >> Dear Hannes,
> > > > > >> >>
> > > > > >> >> Thanks for the quick reply! I've tried changing to LRES and
> > RRES
> > > > and
> > > > > it
> > > > > >> >> seems to just suppress the output:
> > > > > >> >>
> > > > > >> >> FINAL RESULTS
> > > > > >> >>
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> NSTEP ENERGY RMS GMAX
> NAME
> > > > > >> NUMBER
> > > > > >> >> 1 -1.1108E+04 1.3245E+00 1.4038E+01
> HG
> > > > > >> 2021
> > > > > >> >>
> > > > > >> >> BOND = 191.2619 ANGLE = 696.4471 DIHED
> =
> > > > > >> >> 2808.3488
> > > > > >> >> VDWAALS = -2871.4868 EEL = -23739.7079 EPB
> =
> > > > > >> >> -3329.3383
> > > > > >> >> 1-4 VDW = 980.7815 1-4 EEL = 14155.9277 RESTRAINT
> =
> > > > > >> >> 0.0000
> > > > > >> >> ECAVITY = 0.0000 EDISPER = 0.0000
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> CHECK DECOMP - TOTAL ENERGIES (w/ REST)
> > > > > >> >>
> > > > > >> >> INTERNAL= 0.0000
> > > > > >> >> VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> EGB = 0.0000 ESURF = 0.0000
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> CHECK DECOMP - SELF ENERGIES (w/o REST)
> > > > > >> >>
> > > > > >> >> INTERNAL= 0.0000
> > > > > >> >> VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> EGB = 0.0000 ESURF = 0.0000
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> CHECK DECOMP - INDIRECT ENERGIES (w/o
> REST)
> > > > > >> >>
> > > > > >> >> INTERNAL= 0.0000
> > > > > >> >> VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> EGB = 0.0000 ESURF = 0.0000
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> CHECK DECOMP - DIRECT ENERGIES (w/o
> REST)
> > > > > >> >>
> > > > > >> >> INTERNAL= 0.0000
> > > > > >> >> VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> EGB = 0.0000 ESURF = 0.0000
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> CHECK DECOMP - REST ENERGIES
> > > > > >> >>
> > > > > >> >> INTERNAL= 0.0000
> > > > > >> >> VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> EGB = 0.0000 ESURF = 0.0000
> > > > > >> >>
> > > > > >> >>
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> PRINT PAIR DECOMP - TOTAL ENERGIES
> > > > > >> >>
> > > > > >> >> resid1 ->resid2 |internal |vdw |eel |pol
> > |sas
> > > > > >> >>
> > > > >
> > ======================================================================
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> PRINT PAIR DECOMP - SIDECHAIN ENERGIES
> > > > > >> >>
> > > > > >> >> resid1 ->resid2 |internal |vdw |eel |pol
> > |sas
> > > > > >> >>
> > > > >
> > ======================================================================
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> PRINT PAIR DECOMP - BACKBONE ENERGIES
> > > > > >> >>
> > > > > >> >> resid1 ->resid2 |internal |vdw |eel |pol
> > |sas
> > > > > >> >>
> > > > >
> > ======================================================================
> > > > > >> >>
> > > > > >> >> It seems that the values for the internal, electrostatic and
> > vdw
> > > > > >> energies
> > > > > >> >> are actually non-zero in the total output, just for the
> > > > > decomposition
> > > > > >> so I
> > > > > >> >> guess it could be that because the PB breakdown is not
> > > implemented
> > > > > in
> > > > > >> >> AMBER9
> > > > > >> >> - I'm just getting zeroes. Thanks for the help, I might try
> > > > > switching
> > > > > >> to
> > > > > >> >> AMBER10 at some point soon :)
> > > > > >> >>
> > > > > >> >> Best,
> > > > > >> >>
> > > > > >> >> Chris
> > > > > >> >>
> > > > > >> >> 2009/7/28 Hannes Kopitz <Hannes.Kopitz_at_gmx.de>
> > > > > >> >>
> > > > > >> >> > Dear Chris,
> > > > > >> >> >
> > > > > >> >> > A decomposition of the PB reaction field energy is
> > implemented
> > > > > from
> > > > > >> >> AMBER10
> > > > > >> >> > but unfortunately not in AMBER9.
> > > > > >> >> >
> > > > > >> >> > Nevertheless the values for internal, vdw and eel
> shouldn't
> > be
> > > > > zero.
> > > > > >> >> > Just a guess, you should try it with RRES and LRES instead
> of
> > > > RES.
> > > > > >> >> >
> > > > > >> >> > Cheers!
> > > > > >> >> > Hannes
> > > > > >> >> >
> > > > > >> >> > -------- Original-Nachricht --------
> > > > > >> >> > > Datum: Mon, 27 Jul 2009 21:04:14 +0100
> > > > > >> >> > > Von: Chris Whittleston <csw34_at_cam.ac.uk>
> > > > > >> >> > > An: amber_at_ambermd.org
> > > > > >> >> > > Betreff: [AMBER] Using idecomp=3 with igb=10 (PB)
> > > > > >> >> >
> > > > > >> >> > > Dear AMBER users,
> > > > > >> >> > >
> > > > > >> >> > > I'm currently looking at decomposed per-residue
> interaction
> > > > > >> energies
> > > > > >> >> in a
> > > > > >> >> > > protein-ligand system with a GB solvent model (e.g.
> > igb=1/5)
> > > > but
> > > > > >> would
> > > > > >> >> > > like
> > > > > >> >> > > to be able to use Poisson Boltzmann (igb=10) to compare
> > with
> > > > > some
> > > > > >> >> results
> > > > > >> >> > > from an MMPBSA calculation of the same system.
> > > Unfortunately, I
> > > > > am
> > > > > >> >> just
> > > > > >> >> > > getting a huge table of 0.000 for every interaction
> energy.
> > > > > >> >> > >
> > > > > >> >> > > Here is my SANDER input:
> > > > > >> >> > >
> > > > > >> >> > > Interaction energy per residue input for SANDER
> > > > > >> >> > > &cntrl
> > > > > >> >> > > imin = 1,
> > > > > >> >> > > idecomp = 3,
> > > > > >> >> > > ncyc = 1,
> > > > > >> >> > > maxcyc = 1,
> > > > > >> >> > > igb = 10,
> > > > > >> >> > > ntb = 0,
> > > > > >> >> > > cut = 0, <- have also tried 999.9
> > > > > >> >> > > /
> > > > > >> >> > > &pb
> > > > > >> >> > > npopt = 0,
> > > > > >> >> > > radiopt = 0
> > > > > >> >> > > /
> > > > > >> >> > > First set
> > > > > >> >> > > RES -1 318
> > > > > >> >> > > END
> > > > > >> >> > > Second set
> > > > > >> >> > > RES 319
> > > > > >> >> > > END
> > > > > >> >> > > END
> > > > > >> >> > >
> > > > > >> >> > > I am using modified GLYCAM parameters for a sugar
> ligand,
> > > hence
> > > > > >> have
> > > > > >> >> set
> > > > > >> >> > > npopt=0 and radiopt=0. SANDER seems to run ok (it
> doesn't
> > > > > produce
> > > > > >> any
> > > > > >> >> > > warnings or crash out), but after taking 20 seconds or
> so
> > > > > >> calculating
> > > > > >> >> > > things
> > > > > >> >> > > - it produces a table as follows:
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > PRINT PAIR DECOMP - TOTAL ENERGIES
> > > > > >> >> > >
> > > > > >> >> > > resid1 ->resid2 |internal |vdw |eel |pol
> > > > |sas
> > > > > >> >> > >
> > > > > >>
> > > ======================================================================
> > > > > >> >> > > TDC 1-> 1 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 2 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 3 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 4 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 5 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 6 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 7 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 8 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 9 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 10 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 11 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 12 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 13 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 14 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 15 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 16 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 17 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 18 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 19 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 20 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 21 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 22 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 23 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 24 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 25 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 26 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > TDC 1-> 27 0.000 0.000 0.000
> > 0.000
> > > > > >> 0.000
> > > > > >> >> > > ...
> > > > > >> >> > > ...
> > > > > >> >> > > etc (they're all zero)
> > > > > >> >> > >
> > > > > >> >> > > The total energy however is not zero as can be seen in
> the
> > > > > output
> > > > > >> >> above
> > > > > >> >> > > the
> > > > > >> >> > > interaction energy table:
> > > > > >> >> > >
> > > > > >> >> > > NSTEP ENERGY RMS GMAX
> > > NAME
> > > > > >> >> NUMBER
> > > > > >> >> > > 1 -1.1108E+04 1.3245E+00 1.4038E+01
> > > HG
> > > > > >> >> 2021
> > > > > >> >> > >
> > > > > >> >> > > BOND = 191.2619 ANGLE = 696.4471 DIHED
> > > =
> > > > > >> >> > > 2808.3488
> > > > > >> >> > > VDWAALS = -2871.4868 EEL = -23739.7079 EPB
> > > =
> > > > > >> >> > > -3329.3383
> > > > > >> >> > > 1-4 VDW = 980.7815 1-4 EEL = 14155.9277
> > RESTRAINT
> > > =
> > > > > >> >> > > 0.0000
> > > > > >> >> > > ECAVITY = 0.0000 EDISPER = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > Maximum number of minimization cycles reached.
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > FINAL RESULTS
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > NSTEP ENERGY RMS GMAX
> > > NAME
> > > > > >> >> NUMBER
> > > > > >> >> > > 1 -1.1108E+04 1.3245E+00 1.4038E+01
> > > HG
> > > > > >> >> 2021
> > > > > >> >> > >
> > > > > >> >> > > BOND = 191.2619 ANGLE = 696.4471 DIHED
> > > =
> > > > > >> >> > > 2808.3488
> > > > > >> >> > > VDWAALS = -2871.4868 EEL = -23739.7079 EPB
> > > =
> > > > > >> >> > > -3329.3383
> > > > > >> >> > > 1-4 VDW = 980.7815 1-4 EEL = 14155.9277
> > RESTRAINT
> > > =
> > > > > >> >> > > 0.0000
> > > > > >> >> > > ECAVITY = 0.0000 EDISPER = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > CHECK DECOMP - TOTAL ENERGIES (w/
> REST)
> > > > > >> >> > >
> > > > > >> >> > > INTERNAL= 0.0000
> > > > > >> >> > > VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> > > EGB = 0.0000 ESURF = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > CHECK DECOMP - SELF ENERGIES (w/o
> REST)
> > > > > >> >> > >
> > > > > >> >> > > INTERNAL= 0.0000
> > > > > >> >> > > VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> > > EGB = 0.0000 ESURF = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > CHECK DECOMP - INDIRECT ENERGIES
> (w/o
> > > REST)
> > > > > >> >> > >
> > > > > >> >> > > INTERNAL= 0.0000
> > > > > >> >> > > VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> > > EGB = 0.0000 ESURF = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > CHECK DECOMP - DIRECT ENERGIES (w/o
> > > REST)
> > > > > >> >> > >
> > > > > >> >> > > INTERNAL= 0.0000
> > > > > >> >> > > VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> > > EGB = 0.0000 ESURF = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > CHECK DECOMP - REST ENERGIES
> > > > > >> >> > >
> > > > > >> >> > > INTERNAL= 0.0000
> > > > > >> >> > > VDWAALS = 0.0000 EEL = 0.0000
> > > > > >> >> > > EGB = 0.0000 ESURF = 0.0000
> > > > > >> >> > >
> > > > > >> >> > >
> > > > > >> >> > > So - I was wondering if anyone could help me understand
> why
> > > I'm
> > > > > >> just
> > > > > >> >> > > getting
> > > > > >> >> > > zeroes! My one idea so far is that it is not possible to
> > > break
> > > > > down
> > > > > >> >> the
> > > > > >> >> > PB
> > > > > >> >> > > surface energy on a per-atom or per-residue basis and so
> > > SANDER
> > > > > is
> > > > > >> >> > > printing
> > > > > >> >> > > zeros. I'm using AMBER9 with all current bug fixes.
> > > > > >> >> > >
> > > > > >> >> > > Any and all help is greatly appriciated!
> > > > > >> >> > >
> > > > > >> >> > > Chris
> > > > > >> >> > >
> > > > > >> >> > > --
> > > > > >> >> > > Chris Whittleston
> > > > > >> >> > > Department of Chemistry
> > > > > >> >> > > University of Cambridge
> > > > > >> >> > > Lensfield Road, Cambridge, CB2 1EW
> > > > > >> >> > > Email: csw34_at_cam.ac.uk
> > > > > >> >> > > Tel: +44 (0)1223 336423
> > > > > >> >> > > _______________________________________________
> > > > > >> >> > > AMBER mailing list
> > > > > >> >> > > AMBER_at_ambermd.org
> > > > > >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >> >> >
> > > > > >> >> > --
> > > > > >> >> > Neu: GMX Doppel-FLAT mit Internet-Flatrate +
> Telefon-Flatrate
> > > > > >> >> > für nur 19,99 Euro/mtl.!*
> http://portal.gmx.net/de/go/dsl02
> > > > > >> >> >
> > > > > >> >> > _______________________________________________
> > > > > >> >> > AMBER mailing list
> > > > > >> >> > AMBER_at_ambermd.org
> > > > > >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >> >> >
> > > > > >> >>
> > > > > >> >>
> > > > > >> >>
> > > > > >> >> --
> > > > > >> >> Chris Whittleston
> > > > > >> >> Department of Chemistry
> > > > > >> >> University of Cambridge
> > > > > >> >> Lensfield Road, Cambridge, CB2 1EW
> > > > > >> >> Email: csw34_at_cam.ac.uk
> > > > > >> >> Tel: +44 (0)1223 336423
> > > > > >> >> _______________________________________________
> > > > > >> >> AMBER mailing list
> > > > > >> >> AMBER_at_ambermd.org
> > > > > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >> >
> > > > > >> > --
> > > > > >> > Jetzt kostenlos herunterladen: Internet Explorer 8 und
> Mozilla
> > > > > Firefox 3
> > > > > >> -
> > > > > >> > sicherer, schneller und einfacher!
> > > > > >> http://portal.gmx.net/de/go/chbrowser
> > > > > >> >
> > > > > >> > _______________________________________________
> > > > > >> > AMBER mailing list
> > > > > >> > AMBER_at_ambermd.org
> > > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >> >
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --
> > > > > >> Ashish Runthala,
> > > > > >> Faculty Division III,
> > > > > >> Lecturer, Biological Sciences,
> > > > > >> Birla Institute of Technology and Science,
> > > > > >> Pilani, Rajasthan- 333031
> > > > > >> INDIA
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> AMBER mailing list
> > > > > >> AMBER_at_ambermd.org
> > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Chris Whittleston
> > > > > > Department of Chemistry
> > > > > > University of Cambridge
> > > > > > Lensfield Road, Cambridge, CB2 1EW
> > > > > > Email: csw34_at_cam.ac.uk
> > > > > > Tel: +44 (0)1223 336423
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Chris Whittleston
> > > > > Department of Chemistry
> > > > > University of Cambridge
> > > > > Lensfield Road, Cambridge, CB2 1EW
> > > > > Email: csw34_at_cam.ac.uk
> > > > > Tel: +44 (0)1223 336423
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER_at_ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > --
> > > > GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
> > > > Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER_at_ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Chris Whittleston
> > > Department of Chemistry
> > > University of Cambridge
> > > Lensfield Road, Cambridge, CB2 1EW
> > > Email: csw34_at_cam.ac.uk
> > > Tel: +44 (0)1223 336423
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox
> 3.5
> > -
> > sicherer, schneller und einfacher! http://portal.gmx.net/de/go/atbrowser
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Chris Whittleston
> Department of Chemistry
> University of Cambridge
> Lensfield Road, Cambridge, CB2 1EW
> Email: csw34_at_cam.ac.uk
> Tel: +44 (0)1223 336423
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber 

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