dear sir
My structure contain small fragment of protein with drug molecules, which contains 114 atoms. i have successfully run two energy minimization process. unfortunately in case of heating process i have face vlimit exceeded error, i am not able rectify after multiple approaches, My input file is below
Molecular Dynamics(heating)(20ps MD) with restraints on solute
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 15.0,
ntr = 1,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep the solute fixed with weak restraints
10.0
RES 1 88
RES 89 114
END
END
Initially i have set box size (18*18*18*) 5834 squab of angstrom when i gave input file as cut=8.0 angstrom. unfortunetly vlimit exceeded error for step 1.
secondly i have changed ntt=1 as for ntt=3,
Restrain also increase upto 500kcal/mol
i have fixed the constant temprature that is ntb=2, ntp =1 option used
finally time option reduced as dt= 0.0002 option choose
but fragment of protein without dug has been successfullly run upto production, in the case addition add the drug with the fragment of protein when i am facing v limit exceeded error for step 1
the above all tries not succeed to overcome vlimit exceeded error. could you please give suggestion for what i made a mistake and to overcome this problem
my output file shown below
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 05/17/1998 at 23:29:15
[-O]verwriting output
File Assignments:
| MDIN: ab17-21md1.in
| MDOUT: ab17-21md1.out
|INPCRD: ab17-21min2.rst
| PARM: ab17-21wat.top
|RESTRT: ab17-21md1.rst
| REFC: ab17-21min2.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: ab17-21md1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Molecular Dynamics(heating)(20ps MD) with restraints on solute
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 15.0,
ntr = 1,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep the solute fixed with weak restraints
10.0
RES 1 88
RES 89 114
END
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: SGIFFT
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 38.538
| New format PARM file being parsed.
| Version = 1.000 Date = 05/17/98 Time = 17:42:13
NATOM = 40800 NTYPES = 13 NBONH = 40745 MBONA = 57
NTHETH = 130 MTHETA = 76 NPHIH = 223 MPHIA = 130
NHPARM = 0 NPARM = 0 NNB = 54869 NRES = 13563
NBONA = 57 NTHETA = 76 NPHIA = 130 NUMBND = 19
NUMANG = 36 NPTRA = 28 NATYP = 16 NPHB = 1
IFBOX = 1 NMXRS = 114 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2918977
| Hollerith 258365
| Integer 2047399
| Max Pairs 66816800
| Max Rstack 2368794
| Max Istack 204000
| Total 312117 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
MOL
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 1000
iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 15.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Molecular dynamics:
nstlim = 10000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 81.325 Box Y = 77.891 Box Z = 77.076
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 90 NFFT2 = 80 NFFT3 = 80
Cutoff= 15.000 Tol =0.100E-04
Ewald Coefficient = 0.17871
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
MOL
----- READING GROUP 1; TITLE:
Keep the solute fixed with weak restraints
GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
GRP 1 RES 1 TO 88
GRP 1 RES 89 TO 114
Number of atoms in this group = 453
----- END OF GROUP READ -----
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
MOL
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 13562
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2890E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7799E-11 at 2.634640
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 36119819
| TOTAL SIZE OF NONBOND LIST = 36119819
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -184524.8822 EKtot = 0.0000 EPtot = -184524.8822
BOND = 2.7438 ANGLE = 10.0944 DIHED = 37.0235
1-4 NB = 27.9204 1-4 EEL = 0.0000 VDWAALS = 37748.3493
EELEC = -222351.0136 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.2592E-03
------------------------------------------------------------------------------
vlimit exceeded for step 1 ; vmax = 27.120046866612064
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Received on Tue Nov 27 2012 - 22:00:03 PST
