Is that the end of the mdout file you copied into your e-mail? The
************* and NaN energy values is often indicative of some
inconsistency between the prmtop and restrt file. Have you double checked
these with a visualization program to make sure they are the files you think
they are? Also, I noticed you are running the minimization with restraints
on Calcium ions. I would think that if you were using explicit ions that you
would also use explicit water molecules. And finally, was there a specific
reason you chose to use igb=1? I believe igb=5 is more often used than
igb=1, but this should not be causing the errors that you are seeing.
On Thu, Apr 22, 2010 at 4:21 AM, geyan <geyan.big.ac.cn> wrote:
> Hi,Jason
> with the helpful suggestions by you and Bill,I realize I should add the
> at least implicit solvent effect and see what's going on.But when I turn on
> the IGB flag and sets it to 1,the minimization seems crashed.I don't konw
> why,the following is the output of the minimization containing the input
> file for the sander.
> Thank you.
> Amber 10 SANDER 2008
> -------------------------------------------------------
> | Run on 04/22/2010 at 15:58:14
> [-O]verwriting output
> File Assignments:
> | MDIN: min.in
> | MDOUT: min1.out
> |INPCRD: com.crd
> | PARM: com.top
> |RESTRT: min1.rst
> | REFC: com.crd
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
> |INPTRA: inptraj
> |
>
> Here is the input file:
>
> Minimization of the entire molecular system
> &cntrl
> imin=1,
> maxcyc = 5000,
> ncyc = 250,
> ntr = 1,
> cut = 12,
> ntb=0,igb=1,
> ntpr=5,
> drms=0.005,
> &end
> Keep Ca fixed with weak restraints
> 2.0
> FIND
> CA * * *
> SEARCH
> RES 1 247
> END
> END
>
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
> | Flags:
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/09/10 Time = 22:26:16
> NATOM = 4055 NTYPES = 17 NBONH = 1902 MBONA = 2225
> NTHETH = 4311 MTHETA = 3102 NPHIH = 8513 MPHIA = 7264
> NHPARM = 0 NPARM = 0 NNB = 22207 NRES = 247
> NBONA = 2225 NTHETA = 3102 NPHIA = 7264 NUMBND = 54
> NUMANG = 121 NPTRA = 63 NATYP = 30 NPHB = 0
> IFBOX = 0 NMXRS = 33 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
> Implicit solvent radii are modified Bondi radii (mbondi)
> | Memory Use Allocated
> | Real 276403
> | Hollerith 24579
> | Integer 230868
> | Max Pairs 1
> | nblistReal 0
> | nblist Int 0
> | Total 3157 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
> General flags:
> imin = 1, nmropt = 0
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
> Nature and format of output:
> ntxo = 1, ntpr = 5, ntrx = 1, ntwr =
> 500
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
> 0
> Potential function:
> ntf = 1, ntb = 0, igb = 1, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
> saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
> gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500
> rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
> alpb = 0
> scnb = 2.00000, scee = 1.20000
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
> Energy minimization:
> maxcyc = 5000, ncyc = 250, ntmin = 1
> dx0 = 0.01000, drms = 0.00500
> LOADING THE CONSTRAINED ATOMS AS GROUPS
> 5. REFERENCE ATOM COORDINATES
>
> | INFO: Old style inpcrd file read
> ----- READING GROUP 1; TITLE:
> Keep Ca fixed with weak restraints
> GROUP 1 HAS HARMONIC CONSTRAINTS 2.00000
> ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE INCLUDED
> IN GROUP BELOW
> GRAPH NAME = CA SYMBOL = * TREE SYMBOL = * RESIDUE TYPE
> = *
> GRP 1 RES 1 TO 247
> Number of atoms in this group = 225
> ----- END OF GROUP READ -----
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
> begin time read from input coords = 0.000 ps
> Number of triangulated 3-point waters found: 0
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 0.0000E+00 H5T 1
> BOND = 156.7901 ANGLE = 1203.9996 DIHED =
> 2628.4433
> VDWAALS = ************* EEL = -16114.0902 EGB =
> NaN
> 1-4 VDW = 871.3984 1-4 EEL = 4688.0962 RESTRAINT =
> 0.0000
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 5 NaN NaN 0.0000E+00 H5T 1
> BOND = NaN ANGLE = NaN DIHED =
> 12512.1894
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -66813.9317
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> NaN
> EAMBER = NaN
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 NaN NaN 0.0000E+00 H5T 1
> BOND = NaN ANGLE = NaN DIHED =
> 12512.1894
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -66813.9317
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> NaN
> EAMBER = NaN
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 15 NaN NaN 0.0000E+00 H5T 1
> BOND = NaN ANGLE = NaN DIHED =
> 12512.1894
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -66813.9317
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> NaN
> EAMBER = NaN
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 20 NaN NaN 0.0000E+00 H5T 1
> BOND = NaN ANGLE = NaN DIHED =
> 12512.1894
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -66813.9317
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> NaN
> EAMBER = NaN
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 25 NaN NaN 0.0000E+00 H5T 1
> BOND = NaN ANGLE = NaN DIHED =
> 12512.1894
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -66813.9317
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> NaN
> EAMBER = NaN
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 30 NaN NaN 0.0000E+00 H5T 1
> BOND = NaN ANGLE = NaN DIHED =
> 12512.1894
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -66813.9317
> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
> NaN
> EAMBER = NaN
>
>
> 2010-04-22
>
>
>
> geyan
>
>
>
> 发件人： Jason Swails
> 发送时间： 2010-04-21 19:56:47
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: Re: Re: [AMBER] how do MM_PBSA without water
>
> Hello,
> 2010/4/21 geyan <geyan.big.ac.cn>
> > Hi,Bill,sorry to reply you a little late.
> > My system is a complex composed of several moleculars of protein and one
> > molecular of DNA.Because the past study has clearly demonstrated that
> they
> > are interacting with each other without water due to the spore
> enviroment,
> > so I run the simulation in vacuum,without water,in other words,No
> solvent.
> >
> You did not even use implicit solvent (i.e. GB)? Note that while explicit
> water molecules may not be involved in enzyme activity, the solvent almost
> surely plays a role in modulating the secondary and tertiary structure of
> your system, so to neglect it altogether has to be done very carefully. At
> the very least, Amber charges are derived using a protocol that accounts
> for
> increased charge polarization that is typical of polar solvents, so the
> default charge model is not necessarily appropriate for a gas-phase
> simulation. Running gas phase simulations properly are more involved than
> simply changing flags in the sander/pmemd MDIN file, so take care with
> this.
> > Also,I know the MMPBSA calculations used solvent effect,as you
> > say,explicit solvent. But to my special system,I have to turn it
> MM/PBSA does not use explicit solvent. It uses an implicit solvent model
> to
> account for solvation effects. You could conceivably change igb from
> whatever value it's set to to 0 in the _MMPBSA_gb.mdin input file generated
> by MMPBSA (see the -make-mdins and -use-mdins flags in the manual).
> However, I'm pretty sure this will fail with a python "IndexError" when it
> tries to parse non-existent solvation terms (ESURF/EGB).
> As a side note, MM/PB(GB)SA stands for Molecular Mechanics, Poisson
> Boltzmann (or Generalized Born) Surface Area. Vacuum simulations make no
> use of PB, GB, or solvent accessible surface area (which is used to model
> the non-polar solvation energy), so this method does not seem readily
> appropriate to your situation (if indeed vacuum simulations are what you're
> really interested in).
> > off,I don't know whether it will affect the calculation or not?what I'm
> now
> > more interested is how to change the prameters to turn it off,so that it
> can
> > produce a more reasonable result?. Regarding the MMPBSA.py,I have no
> idea
> > with it.I will have a try on google.
> > Best regards.Thank you.
> >
> > You will not find much about it on google, as it is quite new and still
> in
> early stages of development.
> Good luck!
> Jason
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Thu Apr 22 2010 - 04:30:02 PDT
