can you clarify what you are trying to do, and why you think it does not
work?
On Tue, Dec 14, 2010 at 9:24 AM, Giachetti Andrea - CERM <
giachetti.cerm.unifi.it> wrote:
> Hi all, I'm running REM on amber11 and I saw that flag nmropt = 2 are
> not well recognized.
>
> amber11 output:
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | Run on 12/10/2010 at 11:39:43
> [-O]verwriting output
>
> File Assignments:
> | MDIN: sander1.in
> | MDOUT: sander1.out
> |INPCRD: sander0.crd
> | PARM: prmtop
> |RESTRT: sander1.crd
> | REFC: sander0.crd
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: mdinfo
> | MTMD: mtmd
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
> |
>
> Here is the input file:
>
> minimization 2
> &cntrl
> imin=1,
> maxcyc=10000,
> ncyc=1000,
> scee=1.2,
> ntpr=100,
> ntwx=100,
> cut=10.0,
> nmropt=2,
> pencut=0.1,
> ntb=1,
> iscale=5
> /
> &wt type='END' /
> LISTOUT=POUT
> DISANG=allNOE_allDIH.in
>
>
> --------------------------------------------------------------------------------
> 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 = 26.030
> | New format PARM file being parsed.
> | Version = 1.000 Date = 12/10/10 Time = 11:33:47
> NATOM = 16917 NTYPES = 15 NBONH = 16211 MBONA = 716
> NTHETH = 1666 MTHETA = 957 NPHIH = 3197 MPHIA = 2395
> NHPARM = 0 NPARM = 0 NNB = 28589 NRES = 5243
> NBONA = 716 NTHETA = 957 NPHIA = 2395 NUMBND = 37
> NUMANG = 76 NPTRA = 39 NATYP = 26 NPHB = 1
> IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 1100098
> | Hollerith 55996
> | Integer 661984
> | Max Pairs 5639000
> | nblistReal 203004
> | nblist Int 706322
> | Total 37771 kbytes
>
> | Note: 1-4 EEL scale factors were NOT found in the topology file.
> | Using default value of 1.2.
>
> | Note: 1-4 VDW scale factors were NOT found in the topology file.
> | Using default value of 2.0.
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
>
> --------------------------------------------------------------------------------
> 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 = 50, 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 = 1, igb = 0, nsnb
> = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 10000, ncyc = 1000, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 63.760 Box Y = 63.760 Box Z = 63.760
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 64 NFFT2 = 64 NFFT3 = 64
> Cutoff= 8.000 Tol =0.100E-04
> Ewald Coefficient = 0.34864
> Interpolation order = 4
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 5159
>
> Sum of charges from parm topology file = 12.99999994
> Assuming uniform neutralizing plasma
>
>
> --------------------------------------------------------------------------------
> 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 = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 3005380
> | TOTAL SIZE OF NONBOND LIST = 3005380
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -6.4353E+04 1.4282E+00 2.3906E+01 NH2 641
>
> BOND = 4686.9568 ANGLE = 57.6071 DIHED =
> 1112.3451
> VDWAALS = 11098.7681 EEL = -84750.1738 HBOND =
> 0.0000
> 1-4 VDW = 455.0397 1-4 EEL = 2986.2277 RESTRAINT =
> 0.0000
>
>
>
>
> amber10 with some system work well
>
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | Run on 12/10/2010 at 18:36:43
> [-O]verwriting output
>
> File Assignments:
> | MDIN: sander1.in
> | MDOUT: sander1.out
> |INPCRD: sander0.crd
> | PARM: prmtop
> |RESTRT: sander1.crd
> | REFC: sander0.crd
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> |MDINFO: mdinfo
> |INPDIP: inpdip
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
> |
>
> Here is the input file:
>
> minimization 2
> &cntrl
> imin=1,
> maxcyc=1000,
> ncyc=1000,
> scee=1.2,
> ntpr=100,
> ntwx=100,
> cut=10.0,
> nmropt=2,
> pencut=0.1,
> ntb=1,
> iscale=5
> /
> &wt type='END' /
> LISTOUT=POUT
> DISANG=allNOE_allDIH.in
>
>
> --------------------------------------------------------------------------------
> 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 = 26.030
> | New format PARM file being parsed.
> | Version = 1.000 Date = 12/10/10 Time = 11:33:47
> NATOM = 16917 NTYPES = 15 NBONH = 16211 MBONA = 716
> NTHETH = 1666 MTHETA = 957 NPHIH = 3197 MPHIA = 2395
> NHPARM = 0 NPARM = 0 NNB = 28589 NRES = 5243
> NBONA = 716 NTHETA = 957 NPHIA = 2395 NUMBND = 37
> NUMANG = 76 NPTRA = 39 NATYP = 26 NPHB = 1
> IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 1299732
> | Hollerith 106747
> | Integer 630694
> | Max Pairs 9744192
> | nblistReal 203004
> | nblist Int 594146
> | Total 55004 kbytes
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
>
> --------------------------------------------------------------------------------
>
>
>
> General flags:
> imin = 1, nmropt = 2
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 100, ntrx = 1, ntwr
> = 500
> iwrap = 0, ntwx = 100, ntwv = 0, ntwe
> = 0
> 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 = 10.00000, intdiel = 1.00000
> scnb = 2.00000, scee = 1.20000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 1000, ncyc = 1000, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
>
> NMR refinement options:
> iscale = 5, noeskp = 1, ipnlty = 1, mxsub
> = 1
> scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 63.760 Box Y = 63.760 Box Z = 63.760
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 64 NFFT2 = 64 NFFT3 = 64
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> ** No weight changes given **
>
> RESTRAINTS:
> Requested file redirections:
> LISTOUT = POUT
> DISANG = allNOE_allDIH.in
> Restraints will be read from file: allNOE_allDIH.in
> Here are comments from the DISANG input file:
> #NOCORR = FALSE#
> # 2 LYS HA 3 GLN H 3.48
>
> Number of restraints read = 1267
>
> Done reading weight changes/NMR restraints
>
>
> Number of triangulated 3-point waters found: 5159
>
> Sum of charges from parm topology file = 12.99999994
> Assuming uniform neutralizing plasma
>
>
> --------------------------------------------------------------------------------
> 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 = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 5186916
> | TOTAL SIZE OF NONBOND LIST = 5186916
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -5.5343E+04 2.0097E+00 3.2828E+01 C 1388
>
> BOND = 3169.4165 ANGLE = 57.6869 DIHED =
> 1112.4255
> VDWAALS = 4972.9258 EEL = -68121.0240 HBOND =
> 0.0000
> 1-4 VDW = 456.0389 1-4 EEL = 2984.9596 RESTRAINT =
> 24.3697
> EAMBER = -55367.5707
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 24.370
>
> ===============================================================================
>
>
>
>
> Amber11 was compiled using GNU compiler.
>
> Best Regards
>
> Andrea Giachetti
>
> CERM
> University of Florence, Italy
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 14 2010 - 06:30:06 PST
