Re: [AMBER] Problem on nmropt option in amber 11

From: Giachetti Andrea - CERM <giachetti.cerm.unifi.it>
Date: Tue, 14 Dec 2010 15:57:31 +0100

Hi Carlos, I'm trying to minimize a nmr structure using as restraints
the noe and dihedral angles stored in file allNOE_allDIH.in.

If you see the input we turn on nmropt using 2 as value

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

the problem are in the next lines of output where seams that the nmropt
= 2 are not recognized,
also the energy of RESTRAINT during the minimizations remain 0.00000

--------------------------------------------------------------------------------
    2. CONTROL DATA FOR THE RUN

--------------------------------------------------------------------------------



General flags:
      imin = 1,_nmropt = 0_

Nature and format of input:
      ntx = 1, irest = 0, ntrx = 1



using the same input and system in amber10 the nmtopt = 2 are recognized
well and starting energy of restraints = 24.3697

--------------------------------------------------------------------------------
    2. CONTROL DATA FOR THE RUN

--------------------------------------------------------------------------------



General flags:
      imin = 1,_nmropt = 2_

Nature and format of input:
      ntx = 1, irest = 0, ntrx = 1



in attachment you can find the amber input files.

Best Regards
Andrea Giachetti


Il 12/14/2010 03:27 PM, Carlos Simmerling ha scritto:
> 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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>>
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Received on Tue Dec 14 2010 - 07:00:03 PST
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