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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Received on Tue Dec 14 2010 - 06:30:05 PST
