AMBER Archive (2009)

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

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Sun Oct 11 2009 - 16:13:45 CDT

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