[AMBER] AMBER GAUSSIAN QM/MM

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Fri, 24 Oct 2014 15:23:29 +0800

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
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