Dear All,
I want to use the amber/gaussian interface qm/mm method for simulating
mycomplex. however, i come across error " The charge and spin keywords are
deprecated
Please specify charge (qmcharge) and spin multiplicity (spin) in the &qmmm
namelist."
Can anyone guide me to preparing an input file. my input and output file is
as follows:
-------------------------------------------------------------
Here is the input file:
QM/MM
minimisation
&cntrl
imin=1, maxcyc=1000, ncyc=500 ntc=2,
ntf=2,
ntb=0,
cut=20.0,
ifqnt=1
&end
&qmmm
qmmask='.1-31,258-267,273-287,3914-3920,4469-4486'
qmcharge=-1,
qm_theory='EXTERN',
qmshake=1,
qmcut=20.0,
spin=1
&end
&gau
method =
'BLYP',
basis =
'6-31G*',
charge =
-1,
scf_conv =
8,
spinmult =
1,
num_threads =
1,
use_template =
0,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 71.940
| New format PARM file being parsed.
| Version = 1.000 Date = 08/01/14 Time = 10:59:12
NATOM = 141890 NTYPES = 17 NBONH = 137548 MBONA = 4395
NTHETH = 10134 MTHETA = 5960 NPHIH = 20334 MPHIA = 19845
NHPARM = 0 NPARM = 0 NNB = 225995 NRES = 44930
NBONA = 4395 NTHETA = 5960 NPHIA = 19845 NUMBND = 79
NUMANG = 175 NPTRA = 258 NATYP = 44 NPHB = 1
IFBOX = 1 NMXRS = 38 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 8800863
| Hollerith 470602
| Integer 5164564
| Max Pairs 378373333
| nblistReal 1702680
| nblist Int 4853370
| Total 1601050 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
LOADING THE QUANTUM ATOMS AS GROUPS
Mask .1-31,258-267,273-287,3914-3920,4469-4486; matches 81 atoms
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
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 = 2, ntb = 0, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 20.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1000, ncyc = 500, ntmin = 1
dx0 = 0.01000, drms = 0.00010
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
QMMM options:
ifqnt = True nquant = 81
qmgb = 0 qmcharge = -1 adjust_q = 2
spin = 1 qmcut = 20.0000 qmshake = 1
qmmm_int = 1
lnk_atomic_no = 1 lnk_dis = 1.0900 lnk_method = 1
qm_theory = EXTERN verbosity = 0
qmqmdx = Analytical
qm_ewald = 0 qm_pme = False
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 44359
Sum of charges from parm topology file = -0.00000029
Forcing neutrality...
QMMM: ADJUSTING CHARGES
QMMM: ----------------------------------------------------------------------
QMMM: adjust_q = 2
QMMM: Uniformly adjusting the charge of MM atoms to conserve total charge.
QMMM: qm_charge = -1
QMMM: QM atom RESP charge sum (inc MM link) = 2.180
QMMM: Adjusting each MM atom resp charge by = 0.000
QMMM: Sum of MM + QM region is now = -0.000
QMMM: ----------------------------------------------------------------------
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 185854919
| TOTAL SIZE OF NONBOND LIST = 185854919
QMMM: Link Atom Information
QMMM:
------------------------------------------------------------------------
QMMM: nlink = 7 Link Coords Resp Charges
QMMM: MM(typ) - QM(typ) X Y Z MM QM
QMMM: 32 ce 30 c2 74.812 50.496 76.694 -0.039
-0.263
QMMM: 37 c 28 ce 74.156 49.290 75.384 0.711
-0.449
QMMM: 256 C 258 N 78.114 41.161 75.050 0.537
-0.416
QMMM: 268 C 265 2C 81.315 44.963 76.042 0.695
-0.064
QMMM: 288 C 277 CX 76.063 43.848 78.691 0.537
0.040
QMMM: 3911 C8 3914 C8 70.028 46.174 73.674 -0.048
-0.014
QMMM: 4467 CX 4469 CT 71.455 47.526 68.633 -0.027
-0.005
QMMM:
------------------------------------------------------------------------
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 74.8184 46.6707 71.6018
QMMM: 2 2 H 73.8634 46.1788 71.7978
QMMM: 3 3 H 75.4619 45.9684 71.0679
QMMM: 4 4 H 74.6403 47.5331 70.9561
QMMM: 5 5 C 75.4892 47.1137 72.9254
QMMM: 6 6 C 75.7178 45.8400 73.7732
QMMM: 7 7 H 74.7702 45.4311 74.1299
QMMM: 8 8 H 76.3576 46.0546 74.6317
QMMM: 9 9 H 76.2124 45.0637 73.1856
QMMM: 10 10 C 76.8461 47.8193 72.6046
QMMM: 11 11 H 77.5325 47.0749 72.1959
QMMM: 12 12 H 76.6851 48.5478 71.8073
QMMM: 13 13 C 74.5519 48.0779 73.6546
QMMM: 14 14 H 73.8171 48.5842 73.0338
QMMM: 15 15 C 77.4801 48.4782 73.8208
QMMM: 16 16 H 78.0474 47.7982 74.4512
QMMM: 17 17 C 77.3453 49.7503 74.1987
QMMM: 18 18 C 76.5896 50.8273 73.4466
QMMM: 19 19 H 75.8915 51.3399 74.1116
QMMM: 20 20 H 76.0107 50.4404 72.6054
QMMM: 21 21 H 77.2830 51.5815 73.0687
QMMM: 22 22 C 77.9235 50.2170 75.5237
QMMM: 23 23 H 78.9373 49.8247 75.6279
QMMM: 24 24 H 78.0133 51.3048 75.5572
QMMM: 25 25 C 77.1059 49.7371 76.7633
QMMM: 26 26 H 76.9387 48.6580 76.7545
QMMM: 27 27 H 77.7597 49.8813 77.6259
QMMM: 28 28 C 74.7040 48.4570 74.9435
QMMM: 29 29 H 75.4846 48.0158 75.5615
QMMM: 30 30 C 75.8370 50.5477 77.0625
QMMM: 31 31 H 76.0518 51.3076 77.8094
QMMM: 32 258 N 78.3725 42.1958 74.8265
QMMM: 33 259 H 78.1246 42.5431 73.9110
QMMM: 34 260 C 79.1016 43.0943 75.7232
QMMM: 35 261 H 80.0030 42.5820 76.0596
QMMM: 36 262 C 79.5144 44.3365 74.9091
QMMM: 37 263 H 80.0692 44.0176 74.0267
QMMM: 38 264 H 78.6148 44.8430 74.5596
QMMM: 39 265 C 80.3562 45.3503 75.6991
QMMM: 40 266 H 80.5567 46.2008 75.0475
QMMM: 41 267 H 79.7875 45.7115 76.5560
QMMM: 42 273 C 78.2966 43.4638 76.9820
QMMM: 43 274 O 78.7787 43.2679 78.0946
QMMM: 44 275 N 77.0734 43.9763 76.8059
QMMM: 45 276 H 76.7228 44.0264 75.8600
QMMM: 46 277 C 76.2212 44.5467 77.8688
QMMM: 47 278 H 76.7087 45.4241 78.2937
QMMM: 48 279 C 74.9100 44.9939 77.1899
QMMM: 49 280 H 75.1843 45.7522 76.4565
QMMM: 50 281 H 74.5000 44.1365 76.6560
QMMM: 51 282 C 73.7967 45.6175 78.0442
QMMM: 52 283 H 73.4402 44.8752 78.7583
QMMM: 53 284 H 74.2060 46.4665 78.5917
QMMM: 54 285 C 72.6201 46.0830 77.1572
QMMM: 55 286 O 72.3167 45.4403 76.1265
QMMM: 56 287 O 71.9979 47.1402 77.4056
QMMM: 57 3914 C 71.0310 46.6002 73.6582
QMMM: 58 3915 H 71.7584 45.7979 73.7820
QMMM: 59 3916 H 71.1994 47.0908 72.6996
QMMM: 60 3917 N 71.2074 47.5585 74.7717
QMMM: 61 3918 H 71.3925 47.0551 75.6275
QMMM: 62 3919 H 72.0246 48.1420 74.6632
QMMM: 63 3920 H 70.4110 48.1644 74.9088
QMMM: 64 4469 C 71.5940 47.7318 69.6941
QMMM: 65 4470 H 70.6170 47.7380 70.1774
QMMM: 66 4471 H 72.1665 46.9127 70.1294
QMMM: 67 4472 C 72.3028 49.0154 70.0270
QMMM: 68 4473 C 73.3735 49.5221 69.3725
QMMM: 69 4474 H 73.8397 49.0755 68.5067
QMMM: 70 4475 N 73.7452 50.7295 69.9323
QMMM: 71 4476 H 74.4364 51.3477 69.5320
QMMM: 72 4477 C 72.9584 51.0401 71.0181
QMMM: 73 4478 C 72.9476 52.1251 71.9050
QMMM: 74 4479 H 73.6678 52.9226 71.7969
QMMM: 75 4480 C 71.9727 52.1703 72.9147
QMMM: 76 4481 H 71.9371 53.0084 73.5949
QMMM: 77 4482 C 71.0189 51.1402 73.0147
QMMM: 78 4483 H 70.2552 51.1944 73.7764
QMMM: 79 4484 C 71.0478 50.0497 72.1245
QMMM: 80 4485 H 70.2932 49.2807 72.1991
QMMM: 81 4486 C 72.0190 49.9678 71.1012
QMMM: 82 *H 74.8123 50.4956 76.6943
QMMM: 83 *H 74.1565 49.2904 75.3838
QMMM: 84 *H 78.1137 41.1608 75.0496
QMMM: 85 *H 81.3154 44.9628 76.0423
QMMM: 86 *H 76.0631 43.8483 78.6907
QMMM: 87 *H 70.0277 46.1744 73.6737
QMMM: 88 *H 71.4554 47.5264 68.6327
--------------------------------------------------------------------------------
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
| Please also cite the following work for the use of the QM/MM interface:
| A. W. G"otz, M. A. Clark, R. C. Walker
| "An extensible interface for ab initio QM/MM molecular dynamics
simulations
| with AMBER"
| J. Comput. Chem. 2013
| DOI: 10.1002/jcc.23444
Constants for unit conversion taken from
Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730
and using the thermochemical calorie (1 cal = 4.184 J):
A_TO_BOHRS = 1.889726132873E+00
AU_TO_KCAL = 6.2750946943E+02
AU_TO_DEBYE = 2.54174623E+00
>>> Running calculations with Gaussian <<<
SANDER BOMB in subroutine get_namelist (qm2_extern_gau_module)
The charge and spin keywords are deprecated
Please specify charge (qmcharge) and spin multiplicity (spin) in the &qmmm
namelist.
--------------------------------------------------------
Regards
Ayesha Fatima
PhD candidate UM
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Received on Fri Oct 24 2014 - 00:30:02 PDT
