the initial energies are very high and you're restraining the RNA. you might
want to try a short min without restraints in GB before adding water, or
perhaps weakening the restraints (500 is really strong). your bond energies
are getting very high so it looks like the minimization is going badly, you
should try to fix the problem some other way.
On Mon, Sep 15, 2008 at 12:34 PM, <mon_sharma.research.iiit.ac.in> wrote:
> Dear All,
> I am new AMBER10 user. As far as I could understand the manual, and
> tutorial, I prepared one RNA system for doing MD simulations with TIP3P
> water. When I am trying to minimize the system, the minimization stops after
> steepest descent only, and not going further for conjugate gradient. The
> calculation stops abruptly. Moreover when I use SHAKE, it gives LINMIN
> failure, but when I dont use SHAKE, it gives EEL and EAMBER as ********.
> The input file I took as:
>
> input for minimization with restraints
> &cntrl
> imin = 1,
> ntmin = 1,
> dx0 = 0.02,
> maxcyc = 15000,
> ncyc = 7000,
> ntpr = 100,
> ntwr = 100,
> ntwx = 100,
> ntwv = 100,
> ntwe = 100,
> cut = 12,
> iwrap = 1,
> ntt = 3,
> ntr = 1,
> ntb = 1,
> ntc = 1,
> /
> &ewald
> ew_type = 0, verbose =0,
> order = 4
> /
> Hold the RNA fixed
> 500.0
> RES 1 162
> END
> END
>
>
> And the output file is:
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> | peek_ewald_inpcrd: Box info found
> |Largest sphere to fit in unit cell has radius = 37.922
> | New format PARM file being parsed.
> | Version = 1.000 Date = 09/11/08 Time = 21:19:04
> NATOM = 64295 NTYPES = 19 NBONH = 60646 MBONA = 3905
> NTHETH = 4033 MTHETA = 6093 NPHIH = 8994 MPHIA = 11075
> NHPARM = 0 NPARM = 0 NNB = 108007 NRES = 19951
> NBONA = 3905 NTHETA = 6093 NPHIA = 11075 NUMBND = 45
> NUMANG = 88 NPTRA = 41 NATYP = 31 NPHB = 1
> IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
> | Memory Use Allocated
> | Real 4199389
> | Hollerith 405723
> | Integer 1806687
> | Max Pairs 58808493
> | nblistReal 771540
> | nblist Int 2197918
> | Total 285783 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: RECTILINEAR
>
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> -------------------------------------------------------------------------------
> eneral flags:
> imin = 1, 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 = 100
> iwrap = 1, ntwx = 100, ntwv = 100, ntwe = 100
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
>
> Potential function:
> ntf = 1, ntb = 1, igb = 0, nsnb = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
> Energy minimization:
> maxcyc = 15000, ncyc = 7000, ntmin = 1
> dx0 = 0.02000, drms = 0.00010
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 103.434 Box Y = 75.845 Box Z = 104.570
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 108 NFFT2 = 75 NFFT3 = 108
> Cutoff= 12.000 Tol =0.100E-04
> Ewald Coefficient = 0.22664
> Interpolation order = 4
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Hold the RNA fixed
> GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
> GRP 1 RES 1 TO 162
> Number of atoms in this group = 5250
> ----- 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: 19628
>
> Sum of charges from parm topology file = -0.00000014
> 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 = 0.3146E-14 at 2.553520
> | CHECK d/dx switch(x): max rel err = 0.7933E-11 at 2.712040
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 29724073
> | TOTAL SIZE OF NONBOND LIST = 29724073
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.5691E+04 4.7469E+03 1.0290E+06 O 47646
>
> BOND = 185.0610 ANGLE = 6320.6711 DIHED = 3600.1754
> VDWAALS = 144433.7532 EEL = -165420.7272 HBOND = 0.0000
> 1-4 VDW = 3364.2477 1-4 EEL = -18174.1796 RESTRAINT = 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -3.5619E+06 2.3706E+08 6.4100E+10 H2 31370
>
> BOND = 14633.5684 ANGLE = 5112.5799 DIHED = 3723.1738
> VDWAALS = 20229.8168 EEL = -3607696.2833 HBOND = 0.0000
> 1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT = 18115.3132
> EAMBER = -3580011.2945
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 -3.3009E+07 2.9205E+10 7.8970E+12 O 31419
>
> BOND = 14633.5684 ANGLE = 5112.5799 DIHED = 3723.1738
> VDWAALS = 20229.8162 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT = 18115.3132
> EAMBER = *************
>
> ------------------------------
> -------------------------------- and so on the calc to 7000.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 6900 -3.1597E+07 2.6711E+10 7.2226E+12 O 31419
>
> BOND = 14633.5684 ANGLE = 5112.5799 DIHED = 3723.1738
> VDWAALS = 20229.8162 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT = 18115.3132
> EAMBER = *************
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 7000 -1.1928E+07 3.5494E+09 9.5976E+11 H2 31370
>
> BOND = 14633.5684 ANGLE = 5112.5799 DIHED = 3723.1738
> VDWAALS = 20229.8164 EEL = ************* HBOND = 0.0000
> 1-4 VDW = 2341.3391 1-4 EEL = -18355.4891 RESTRAINT = 18115.3132
> EAMBER = *************
>
>
> and here the calculation stops. I am missing something. But can't figure
> out what. If anyone can please help me out..
> Thanking you,
> Regards,
> Monika
>
>
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Wed Sep 17 2008 - 03:08:20 PDT
