Thanks Hannes, that has certainly cleared things up a bit. I see you point
about the per-residue interaction energy (including interactions to all
other residues and self) being more relevent to overall binding than a
pairwise decompositoon. Makes a lot of sense. I think that I actually want
to know about both! I'm not predicting hot-spots per-se as the system I work
on has a well defined binding site, but it will be interesting to see what
difference taking all interactions makes to my analysis.
Thanks again for all your help,
Chris
2009/10/12 Hannes Kopitz <Hannes.Kopitz.gmx.de>
> 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.cam.ac.uk>
> > An: AMBER Mailing List <amber.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.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.cam.ac.uk>
> > > > An: AMBER Mailing List <amber.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.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.cam.ac.uk>
> > > > > > An: AMBER Mailing List <amber.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.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.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.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.cam.ac.uk>
> > > > > > >> >> An: AMBER Mailing List <amber.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.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.cam.ac.uk>
> > > > > > >> >> > > An: amber.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.cam.ac.uk
> > > > > > >> >> > > Tel: +44 (0)1223 336423
> > > > > > >> >> > > _______________________________________________
> > > > > > >> >> > > AMBER mailing list
> > > > > > >> >> > > AMBER.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.ambermd.org
> > > > > > >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >> >> >
> > > > > > >> >>
> > > > > > >> >>
> > > > > > >> >>
> > > > > > >> >> --
> > > > > > >> >> Chris Whittleston
> > > > > > >> >> Department of Chemistry
> > > > > > >> >> University of Cambridge
> > > > > > >> >> Lensfield Road, Cambridge, CB2 1EW
> > > > > > >> >> Email: csw34.cam.ac.uk
> > > > > > >> >> Tel: +44 (0)1223 336423
> > > > > > >> >> _______________________________________________
> > > > > > >> >> AMBER mailing list
> > > > > > >> >> AMBER.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.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.ambermd.org
> > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Chris Whittleston
> > > > > > > Department of Chemistry
> > > > > > > University of Cambridge
> > > > > > > Lensfield Road, Cambridge, CB2 1EW
> > > > > > > Email: csw34.cam.ac.uk
> > > > > > > Tel: +44 (0)1223 336423
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Chris Whittleston
> > > > > > Department of Chemistry
> > > > > > University of Cambridge
> > > > > > Lensfield Road, Cambridge, CB2 1EW
> > > > > > Email: csw34.cam.ac.uk
> > > > > > Tel: +44 (0)1223 336423
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.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.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Chris Whittleston
> > > > Department of Chemistry
> > > > University of Cambridge
> > > > Lensfield Road, Cambridge, CB2 1EW
> > > > Email: csw34.cam.ac.uk
> > > > Tel: +44 (0)1223 336423
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.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.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Chris Whittleston
> > Department of Chemistry
> > University of Cambridge
> > Lensfield Road, Cambridge, CB2 1EW
> > Email: csw34.cam.ac.uk
> > Tel: +44 (0)1223 336423
> > _______________________________________________
> > AMBER mailing list
> > AMBER.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.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chris Whittleston
Department of Chemistry
University of Cambridge
Lensfield Road, Cambridge, CB2 1EW
Email: csw34.cam.ac.uk
Tel: +44 (0)1223 336423
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Received on Tue Oct 13 2009 - 03:30:02 PDT
