did you want to restrain the CA atoms? there is a group restraint listed
but you didn't use ntr=1 so it is ignored. if you use them, 10 might be
too large
for a force constant, try 1.0 if you have trouble.
otherwise I don't see a problem but maybe someone who uses LD for
temperature ramping may spot something.
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Madalin Giambasu wrote:
>
>This are the first steps of the simulation. I killed this job, but I can
>provide , if there is need, a longer output.
>
>
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
>| Run on 08/30/2004 at 10:18:44
> [-O]verwriting output
>
>File Assignments:
>| MDIN: heat+eqln.inp
>| MDOUT: mdout
>|INPCRD: x_na1.rst
>| PARM: x_na.prmtop
>|RESTRT: x_na2_lent_ca.rst
>| REFC: x_na1.rst
>| MDVEL: mdvel
>| MDEN: mden
>| MDCRD: mdcrd
>|MDINFO: mdinfo
>|INPDIP: inpdip
>|RSTDIP: rstdip
>
>
> Here is the input file:
>
>Molecular dynamics script
> &cntrl
> imin=0
> nstlim=400000, ntt=3,gamma_ln=1,
> ntpr=50, pencut=0.1, ntwx = 50,
> ntwe =50,
> cut=16,
> vlimit=10,
> ntb=0,
> ntc=2, nmropt=1,
> &end
> constrain ca
> 10
> search
> CA * M *
> find
> end
> end
> &ewald
> eedmeth=5
> &end
> &wt
> type='TEMP0', istep1=0, istep2=35000, value1=0.0, value2=100.0, /
> &wt
> type='TEMP0', istep1=35001, istep2=70000, value1=100.0, value2=200.0, /
> &wt
> type='TEMP0', istep1=70001, istep2=100000, value1=200.0, value2=300.0,
>/
> &wt
> type='TEMP0', istep1=100001, istep2=400000, value1=300.0, value2=300.0,
>/
> &wt
> type='END' /
>
>--------------------------------------------------------------------------------
> 1. RESOURCE USE:
>--------------------------------------------------------------------------------
>
>| Flags:
>| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
>|Largest sphere to fit in unit cell has radius = 66.526
>| New format PARM file being parsed.
>| Version = 1.000 Date = 08/24/04 Time = 11:43:08
> NATOM = 6304 NTYPES = 15 NBONH = 3047 MBONA = 3330
> NTHETH = 7062 MTHETA = 4535 NPHIH = 13354 MPHIA = 9745
> NHPARM = 0 NPARM = 0 NNB = 35072 NRES = 430
> NBONA = 3330 NTHETA = 4535 NPHIA = 9745 NUMBND = 43
> NUMANG = 93 NPTRA = 49 NATYP = 30 NPHB = 0
> IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
>| Memory Use Allocated
>| Real 415754
>| Hollerith 38256
>| Integer 1455716
>| Max Pairs 12254976
>| Max Rstack 113040
>| Max Istack 31520
>| Total 57961 kbytes
>| Duplicated 0 dihedrals
>| Duplicated 0 dihedrals
>
>--------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>--------------------------------------------------------------------------------
>
>
>
>General flags:
> imin = 0, nmropt = 1
>
>Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
>Nature and format of output:
> ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
>500
> iwrap = 0, ntwx = 50, ntwv = 0, ntwe =
>50
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
>0
>
>Potential function:
> ntf = 1, ntb = 0, igb = 0, nsnb =
>25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 16.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
>Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
>Molecular dynamics:
> nstlim = 400000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00100, vlimit = 10.00000
>
>Langevin dynamics temperature regulation:
> ig = 71277
> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
>
>SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
>NMR refinement options:
> iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
>1
> scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>
>--------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>--------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TEMP0 0 35000 0.000000 100.000000 0 0
> TEMP0 35001 70000 100.000000 200.000000 0 0
> TEMP0 70001 100000 200.000000 300.000000 0 0
> TEMP0 100001 400000 300.000000 300.000000 0 0
>
> RESTRAINTS:
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = -0.00000047
> Forcing neutrality...
>
>--------------------------------------------------------------------------------
> 4. RESULTS
>--------------------------------------------------------------------------------
>
> ---------------------------------------------------
>
> eedmeth=5: Using 1/r dielectric
>
> ---------------------------------------------------
>| Local SIZE OF NONBOND LIST = 3224429
>| TOTAL SIZE OF NONBOND LIST = 3224429
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
>0.0
> Etot = -3810.6919 EKtot = 0.0000 EPtot =
>-3810.6919
> BOND = 218.8366 ANGLE = 951.6952 DIHED =
>3936.4964
> 1-4 NB = 1276.1936 1-4 EEL = 6371.2105 VDWAALS =
>-2448.1057
> EELEC = -14117.0186 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 15.22 PRESS =
>0.0
> Etot = -3304.0423 EKtot = 239.8629 EPtot =
>-3543.9052
> BOND = 206.7875 ANGLE = 1054.7072 DIHED =
>3959.0853
> 1-4 NB = 1289.0443 1-4 EEL = 6367.8200 VDWAALS =
>-2479.8637
> EELEC = -13941.4858 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 28.32 PRESS =
>0.0
> Etot = -2859.1804 EKtot = 446.3120 EPtot =
>-3305.4924
> BOND = 255.9120 ANGLE = 1172.4957 DIHED =
>3979.4847
> 1-4 NB = 1289.9858 1-4 EEL = 6363.3274 VDWAALS =
>-2481.6255
> EELEC = -13885.0725 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 150 TIME(PS) = 0.150 TEMP(K) = 41.17 PRESS =
>0.0
> Etot = -2465.8044 EKtot = 648.7614 EPtot =
>-3114.5659
> BOND = 302.9045 ANGLE = 1277.1544 DIHED =
>4016.1194
> 1-4 NB = 1293.2318 1-4 EEL = 6365.1019 VDWAALS =
>-2467.1688
> EELEC = -13901.9090 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 53.06 PRESS =
>0.0
> Etot = -2085.7407 EKtot = 836.0203 EPtot =
>-2921.7610
> BOND = 353.6672 ANGLE = 1361.9579 DIHED =
>4046.4720
> 1-4 NB = 1293.5304 1-4 EEL = 6369.6712 VDWAALS =
>-2434.4922
> EELEC = -13912.5674 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 250 TIME(PS) = 0.250 TEMP(K) = 66.68 PRESS =
>0.0
> Etot = -1695.4135 EKtot = 1050.6658 EPtot =
>-2746.0793
> BOND = 380.6981 ANGLE = 1452.2613 DIHED =
>4059.9768
> 1-4 NB = 1312.0277 1-4 EEL = 6366.0306 VDWAALS =
>-2461.5100
> EELEC = -13855.5637 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 300 TIME(PS) = 0.300 TEMP(K) = 78.52 PRESS =
>0.0
> Etot = -1300.9163 EKtot = 1237.3369 EPtot =
>-2538.2532
> BOND = 434.9664 ANGLE = 1567.9427 DIHED =
>4093.2816
> 1-4 NB = 1306.9961 1-4 EEL = 6360.8800 VDWAALS =
>-2460.6108
> EELEC = -13841.7092 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 350 TIME(PS) = 0.350 TEMP(K) = 89.48 PRESS =
>0.0
> Etot = -919.6005 EKtot = 1410.0507 EPtot =
>-2329.6513
> BOND = 474.8886 ANGLE = 1643.6900 DIHED =
>4120.2951
> 1-4 NB = 1319.6168 1-4 EEL = 6367.5290 VDWAALS =
>-2449.8313
> EELEC = -13805.8394 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
> NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 100.42 PRESS =
>0.0
> Etot = -596.9411 EKtot = 1582.3260 EPtot =
>-2179.2671
> BOND = 493.7875 ANGLE = 1722.6750 DIHED =
>4124.0786
> 1-4 NB = 1325.3619 1-4 EEL = 6382.6767 VDWAALS =
>-2434.9758
> EELEC = -13792.8710 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>===============================================================================
>
>
>-------------------------------------------------------
>Madalin G. Giambasu
>Junior Research Assistant
>Institute of Biochemistry of Romanian Academy of Science
>Splaiul Independentei 296, 060031, Bucharest 17, Romania
>Phone: (+4)021.223.90.69; FAX: (+4)021.223.90.68
>
>-------------------------------------------------------
>
>
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>
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Received on Thu Sep 02 2004 - 01:15:12 PDT
