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 - 01:30:03 PDT
