Thank you for the prompt response.
On Fri, Oct 24, 2014 at 4:07 PM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Hi,
> The error message seems pretty clear to me:
> You already have specified charge (qmcharge) and spin multiplicity (spin)
> in the &qmmm
> namelist, so just remove them (charge, spinmult) from the &gau namelist.
> --Marc
>
> On 24 October 2014 08:23, Ayesha Fatima <ayeshafatima.69.gmail.com> wrote:
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
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Received on Fri Oct 24 2014 - 02:00:02 PDT
