The calculation is not assuming that you have run your simulation with
explicit water molecules, but is running the calculation using an implicit
solvent (i.e. setting IGB=2). You said that you want the calculation to
remove "the solvent effect to fit your system"? Did you run the simulation
in vacuum? Do you want the calculation to be done assuming NO solvent,
implicit or explicit? Or did you run it with some sort of implicit solvent?
Typically MMPBSA calculations are performed on simulations that have used
explicit solvent, even though the calculation itself does not [typically]
include the explicit water molecules in the calculation. This has been
previously shown to give better results.
On a side note, have you tried running the calculation with MMPBSA.py? I
wonder if there is a warning or error in that script that might help us
elucidate the problem, also.
-Bill
2010/4/19 geyan <geyan.big.ac.cn>
> Hi Bill,
> when I do the binding energy analysis according to the default parameters
> of the "binding_energy.mmpbsa",I got the following output which is obviously
> wrong by just simply looking at the PBTOT/GBTOT items,which is positive. In
> my opinion,the input file with the defaulted parameter think my system is
> containing water,but in fact,I do the MD without water,this may confuse the
> program and producing the following error output. So,I think it's necessary
> to reset the input file by clearly removing the solvent effect to fit my
> system.
> Am I right?How to change?Can you show me?
> Appreciate your help and anyone's suggestions.
>
>
> # COMPLEX RECEPTOR LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -8193.05 51.48 -131.16 19.18 -7785.84
> 34.73
> VDW -761.68 31.98 -147.03 9.21 -658.66
> 23.16
> INT 7395.87 51.63 1571.08 32.22 5824.80
> 53.48
> GAS -1558.86 63.70 1292.89 33.45 -2619.71
> 55.94
> PBSUR 79.24 0.49 32.05 0.14 95.23
> 0.53
> PBCAL -7424.03 35.66 -5696.36 14.59 -2440.93
> 21.73
> PBSOL -7344.79 35.54 -5664.31 14.63 -2345.70
> 21.59
> PBELE -15617.09 36.70 -5827.51 12.52 -10226.78
> 25.83
> PBTOT -8903.66 51.53 -4371.42 29.87 -4965.41
> 53.64
> GBSUR 79.24 0.49 32.05 0.14 95.23
> 0.53
> GB -7883.39 39.75 -5539.42 15.01 -2644.02
> 21.35
> GBSOL -7804.15 39.68 -5507.37 15.04 -2548.78
> 21.19
> GBELE -16076.45 28.35 -5670.58 12.01 -10429.86
> 24.55
> GBTOT -9363.02 46.60 -4214.48 30.63 -5168.49
> 52.04
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -276.05 41.90
> VDW 44.01 18.72
> INT -0.00 0.00
> GAS -232.04 42.51
> PBSUR -48.04 0.25
> PBCAL 713.26 32.95
> PBSOL 665.22 32.95
> PBELE 437.20 23.69
> PBTOT 433.17 27.53
> GBSUR -48.04 0.25
> GB 300.04 37.71
> GBSOL 252.00 37.73
> GBELE 23.99 16.29
> GBTOT 19.96 23.16
>
>
> > .GENERAL
> > PREFIX snapshot
> > PATH ./
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ./ras-raf.prmtop
> > RECPT ./ras.prmtop
> > LIGPT ./raf.prmtop
> > GC 0
> > AS 0
> > DC 0
> > MM 1
> > GB 1
> > PB 1
> > MS 1
> > NM 0
> > .PB
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2
> > LINIT 1000
> > PRBRAD 1.4
> > ISTRNG 0.0
> > RADIOPT 0
> > NPOPT 1
> > CAVITY_SURFTEN 0.0072
> > CAVITY_OFFSET 0.00
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MM
> > DIELC 1.0
> > .GB
> > IGB 2
> > GBSA 1
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MS
> > PROBE 0.0
> > .PROGRAMS
> 2010-04-19
>
>
>
> geyan
>
>
>
> 发件人： Bill Miller III
> 发送时间： 2010-04-18 23:37:57
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: Re: [AMBER] how do MM_PBSA without water
>
> Most of these parameters should be fine for your simulation, but can be
> adjusted based on your specific needs for your system. In general, these
> default values should be okay, but you should look into them and do a
> literature research, if necessary. Regarding the dielectric constants
> (internal and external), a value of one has been to shown to work well for
> the internal value of proteins, and the external value of 80 is typical if
> the solvent being modeled is water. You may also want to look at adjusting
> the ISTRNG and SALTCON depending the salt concentration you want to
> consider
> for your calculation.
> I hope that helps.
> -Bill
> On Sun, Apr 18, 2010 at 11:20 AM, geyan <geyan.big.ac.cn> wrote:
> > Hi,Bill,thank you
> > so far,I can only master the mm_pbsa.pl script.You have told me how to
> > set the parameters of the extracting step.Now do I need change anything
> of
> > the following binding calculation input file to fit my no water system to
> > generate the accurate binding energy result? I read from the explaination
> > that some items is used to set the solvent effect,for example, "EXDI -
> > Dielectric constant for the surrounding solvent".In fact,I am not
> familiar
> > with these even I study carefully of every item.
> > so,can you kindly tell me how to change these parameters if it is
> > necessary,of courese,except the prmtop file.
> > really appreciate your help.
> >
> > .GENERAL
> > PREFIX snapshot
> > PATH ./
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ./ras-raf.prmtop
> > RECPT ./ras.prmtop
> > LIGPT ./raf.prmtop
> > GC 0
> > AS 0
> > DC 0
> > MM 1
> > GB 1
> > PB 1
> > MS 1
> > NM 0
> > .PB
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 2
> > LINIT 1000
> > PRBRAD 1.4
> > ISTRNG 0.0
> > RADIOPT 0
> > NPOPT 1
> > CAVITY_SURFTEN 0.0072
> > CAVITY_OFFSET 0.00
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MM
> > DIELC 1.0
> > .GB
> > IGB 2
> > GBSA 1
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > .MS
> > PROBE 0.0
> > .PROGRAMS
> >
> > 2010-04-18
> >
> >
> >
> > geyan
> >
> >
> >
> > 发件人： Bill Miller III
> > 发送时间： 2010-04-18 21:20:18
> > 收件人： AMBER Mailing List
> > 抄送：
> > 主题： Re: [AMBER] how do MM_PBSA without water
> >
> > Simply adding 'intial_traj=1' in the &general namelist of the MMPBSA.py
> > input file will take care of this for you.
> > This isn't much more complicated using mm_pbsa.pl either. In the
> .MAKECRD
> > section make sure you set 'BOX' as 'NO' and then just fill in the rest of
> > the information as explained in the AMBER Manual (start frame, end frame,
> > ligand atom numbers, receptor atom numbers, etc). Note that this section
> is
> > only used when generating snapshots (GC) is turned on (i.e. set to 1).
> > Good luck!
> > -Bill
> > On Sun, Apr 18, 2010 at 3:48 AM, geyan <geyan.big.ac.cn> wrote:
> > > Dear Amber users,
> > > I have got the trajectory of a system of DNA-Protein complex.
> Because
> > I
> > > konw they'are interacting with each other without water in nature,so I
> > > didn't add solvent effect.Now the problem is,how I alter the script
> from
> > the
> > > Amber Tutorial of MM_pbsa to extract snapshot and do the accurate PBSA
> > > analysis.The standard input of the two scripts is a little too complex
> > for
> > > me to change,it has beyond my scope.
> > > Any help is appreciated
> > >
> > >
> > > 2010-04-18
> > >
> > >
> > >
> > > geyan
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 19 2010 - 06:30:03 PDT
