AMBER Archive (2009)

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

From: Chris Whittleston (csw34_at_cam.ac.uk)
Date: Thu Oct 08 2009 - 05:47:22 CDT

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
>> >
>> > --
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>> >
>>
>>
>>
>> --
>> 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
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