AMBER Archive (2009)

Subject: Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala

From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed Nov 11 2009 - 16:30:35 CST

Hello,

As for confirmation about /bin/sh, I too use Ubuntu. The first thing I did
when I began setting up my environment was to redirect /bin/sh to /bin/bash
rather than /bin/dash, since it causes a lot of headaches. You could, of
course, go through the Amber source tree and change #!/bin/sh to #!/bin/bash
to make it use the proper shell, but this issue is pervasive enough that I
think it is worth changing /bin/sh permanently.

If you google "Bad fd number", you will see countless hits of people saying
"Ubuntu links /bin/sh to dash rather than bash." (since /bin/sh is a
symbolic link to /bin/dash). The almost unanimous fix for this issue is
something along the lines of "sudo rm /bin/sh; sudo ln -s /bin/bash /bin/sh"
to make /bin/sh point to /bin/bash. It would be worth seeing if this fixes
the issue.

Any script that uses #!/bin/csh should be fine since it explicitly calls
cshell as long as you have cshell installed (which Ubuntu does NOT come with
by default, but can be obtained via apt-get install csh). Same with
#!/bin/bash.

Hope this helps,
Jason

On Wed, Nov 11, 2009 at 5:04 PM, Wallace Kunin <kunin_at_marshall.edu> wrote:

> This is antechamber.out:
>
> Total number of electrons: 58; net charge: 0
> >
> > Running: /home/kunin/amber10/bin/mopac.sh
> > ln: creating hard link `FOR005': File exists
> > /home/kunin/amber10/bin/mopac.sh: 12: Syntax error: Bad fd number
> > Error: cannot run "/home/kunin/amber10/bin/mopac.sh" of bcc() in charge.c
> > properly, exit
> >
>
> This is FOR005:
>
> AM1 ANALYT MMOK GEO-OK PRECISE CHARGE=0
> > created by wmopcrt() for mopac
> >
> > C -1.9590 1 0.1020 1 0.7950 1
> > C -1.2490 1 0.6020 1 -0.3030 1
> > C -2.0710 1 0.8650 1 1.9630 1
> > C -0.6460 1 1.8630 1 -0.2340 1
> > C -1.4720 1 2.1290 1 2.0310 1
> > C -0.7590 1 2.6270 1 0.9340 1
> > H -1.5580 1 2.7190 1 2.9310 1
> > S -2.7820 1 0.3650 1 3.0600 1
> > H -3.5410 1 0.9790 1 3.2740 1
> > H -0.7870 1 -0.0430 1 -0.9380 1
> > H 0.3730 1 2.0450 1 -0.7840 1
> > H -0.0920 1 3.5780 1 0.7810 1
> > H -2.3790 1 -0.9160 1 0.9010 1
> >
>
> I have no mopac.out in the $AMBEHROME/test/antechamber/tp directory. This
> is mopac.out.save:
>
>
> *******************************************************************************
> > ** FRANK J. SEILER RES. LAB., U.S. AIR FORCE ACADEMY, COLO. SPGS., CO.
> > 80840 **
> >
> >
> *******************************************************************************
> >
> > AM1 CALCULATION RESULTS
> >
> >
> >
> >
> *******************************************************************************
> > * MOPAC: VERSION 6.00
> > CALC'D.
> > * GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK
> > * MMOK - APPLY MM CORRECTION TO CONH BARRIER
> > * ANALYT - USE ANALYTIC DERIVATIVES
> > *
> > *
> > *
> > * CHARGE ON SYSTEM = 0
> > *
> > *
> > *
> > * T= - A TIME OF 3600.0 SECONDS REQUESTED
> > * DUMP=N - RESTART FILE WRITTEN EVERY 3600.0 SECONDS
> > * AM1 - THE AM1 HAMILTONIAN TO BE USED
> > * PRECISE - CRITERIA TO BE INCREASED BY 100 TIMES
> >
> >
> ***********************************************************************100BY100
> > AM1 ANALYT MMOK GEO-OK PRECISE CHARGE=0
> > created by wmopcrt() for mopac
> >
> >
> > ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
> > NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
> > (I) NA:I NB:NA:I NC:NB:NA:I NA
> > NB NC
> >
> > 1 C
> > 2 C 1.39989 * 1
> > 3 C 1.39962 * 120.02782 * 1 2
> > 4 C 1.39946 * 120.11216 * 0.22108 * 2
> > 1 3
> > 5 C 1.40040 * 119.89048 * 0.00000 * 3
> > 1 2
> > 6 C 1.39992 * 120.05865 * -0.18829 * 5
> > 3 1
> > 7 H 1.07958 * 119.97913 * 179.96264 * 5
> > 3 1
> > 8 S 1.39962 * 119.99869 * 179.94373 * 3
> > 1 2
> > 9 H 0.99944 * 109.52035 * -119.93296 * 8
> > 3 1
> > 10 H 1.01622 * 119.60329 * 150.72783 * 2
> > 1 3
> > 11 H 1.17217 * 119.42914 * 145.09497 * 4
> > 2 1
> > 12 H 1.17162 * 132.92409 * -172.73089 * 6
> > 5 3
> > 13 H 1.10633 * 126.60875 * -172.93726 * 1
> > 2 3
> >
> >
> > CARTESIAN COORDINATES
> >
> > NO. ATOM X Y Z
> >
> > 1 C 0.0000 0.0000 0.0000
> > 2 C 1.3999 0.0000 0.0000
> > 3 C -0.7004 1.2118 0.0000
> > 4 C 2.1020 1.2106 0.0047
> > 5 C 0.0015 2.4235 0.0000
> > 6 C 1.4014 2.4230 0.0040
> > 7 H -0.5373 3.3591 -0.0006
> > 8 S -2.1000 1.2111 -0.0012
> > 9 H -2.4335 1.6813 -0.8176
> > 10 H 1.9019 -0.7707 0.4320
> > 11 H 3.1152 1.2865 0.5892
> > 12 H 2.1994 3.2739 0.1134
> > 13 H -0.6598 -0.8813 0.1092
> > H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909
> > (1985)
> > C: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909
> > (1985)
> > S: (AM1): M.J.S.DEWAR, Y-C YUAN, THEOCHEM, IN
> > PRESS
> >
> >
> > RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 18
> >
> >
> > INTERATOMIC DISTANCES
> > 0
> > C 1 C 2 C 3 C 4 C 5
> C
> > 6
> >
> >
> ------------------------------------------------------------------------------
> > C 1 0.000000
> > C 2 1.399894 0.000000
> > C 3 1.399620 2.424791 0.000000
> > C 4 2.425682 1.399461 2.802399 0.000000
> > C 5 2.423550 2.798038 1.400400 2.425542 0.000000
> > C 6 2.799097 2.422993 2.425867 1.400246 1.399922
> > 0.000000
> > H 7 3.401762 3.877619 2.153488 3.403190 1.079581
> > 2.152876
> > S 8 2.424195 3.703515 1.399618 4.202016 2.426239
> > 3.705273
> > H 9 3.068761 4.265011 1.972972 4.633416 2.673719
> > 3.991485
> > H 10 2.097117 1.016216 3.299837 2.036746 3.741861
> > 3.260917
> > H 11 3.421508 2.223622 3.861547 1.172171 3.366745
> > 2.137992
> > H 12 3.945689 3.371994 3.560047 2.068450 2.359343
> > 1.171622
> > H 13 1.106327 2.242953 2.096347 3.466173 3.372167
> > 3.895923
> > 0
> > H 7 S 8 H 9 H 10 H 11
> H
> > 12
> >
> >
> ------------------------------------------------------------------------------
> > H 7 0.000000
> > S 8 2.656338 0.000000
> > H 9 2.660451 0.999436 0.000000
> > H 10 4.815807 4.486702 5.135167 0.000000
> > H 11 4.240746 5.249072 5.737867 2.393545 0.000000
> > H 12 2.740353 4.770036 4.986656 4.068044 2.239362
> > 0.000000
> > H 13 4.243596 2.542568 3.251522 2.584282 4.379526
> > 5.043865
> > 0
> > H 13
> > ------------------
> > H 13 0.000000
> > CYCLE: 1 TIME: 0.04 TIME LEFT: 3599.9 GRAD.: 764.818 HEAT:
> > 80.79812
> > CYCLE: 2 TIME: 0.04 TIME LEFT: 3599.9 GRAD.: 145.658 HEAT:
> > 44.26782
> > CYCLE: 3 TIME: 0.05 TIME LEFT: 3599.8 GRAD.: 149.233 HEAT:
> > 38.08355
> > CYCLE: 4 TIME: 0.03 TIME LEFT: 3599.8 GRAD.: 183.779 HEAT:
> > 34.88734
> > CYCLE: 5 TIME: 0.03 TIME LEFT: 3599.8 GRAD.: 173.298 HEAT:
> > 32.39184
> > CYCLE: 6 TIME: 0.02 TIME LEFT: 3599.8 GRAD.: 122.647 HEAT:
> > 30.74605
> > CYCLE: 7 TIME: 0.05 TIME LEFT: 3599.7 GRAD.: 49.110 HEAT:
> > 28.82368
> > CYCLE: 8 TIME: 0.02 TIME LEFT: 3599.7 GRAD.: 47.651 HEAT:
> > 27.57849
> > CYCLE: 9 TIME: 0.02 TIME LEFT: 3599.7 GRAD.: 69.685 HEAT:
> > 27.00719
> > CYCLE: 10 TIME: 0.02 TIME LEFT: 3599.6 GRAD.: 28.723 HEAT:
> > 26.68135
> > CYCLE: 11 TIME: 0.02 TIME LEFT: 3599.6 GRAD.: 16.410 HEAT:
> > 26.07702
> > CYCLE: 12 TIME: 0.05 TIME LEFT: 3599.6 GRAD.: 27.417 HEAT:
> > 25.99498
> > CYCLE: 13 TIME: 0.05 TIME LEFT: 3599.5 GRAD.: 35.170 HEAT:
> > 25.98831
> > CYCLE: 14 TIME: 0.03 TIME LEFT: 3599.5 GRAD.: 29.912 HEAT:
> > 25.95094
> > CYCLE: 15 TIME: 0.05 TIME LEFT: 3599.4 GRAD.: 25.086 HEAT:
> > 25.94838
> > CYCLE: 16 TIME: 0.02 TIME LEFT: 3599.4 GRAD.: 20.134 HEAT:
> > 26.59378
> > CYCLE: 17 TIME: 0.02 TIME LEFT: 3599.4 GRAD.: 21.010 HEAT:
> > 25.94016
> > CYCLE: 18 TIME: 0.02 TIME LEFT: 3599.4 GRAD.: 12.686 HEAT:
> > 25.89256
> > CYCLE: 19 TIME: 0.02 TIME LEFT: 3599.3 GRAD.: 10.171 HEAT:
> > 25.84763
> > HEAT OF FORMATION TEST SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 20 TIME: 0.02 TIME LEFT: 3599.3 GRAD.: 11.541 HEAT:
> > 25.84615
> > CYCLE: 21 TIME: 0.02 TIME LEFT: 3599.3 GRAD.: 11.885 HEAT:
> > 25.84054
> > CYCLE: 22 TIME: 0.02 TIME LEFT: 3599.3 GRAD.: 9.638 HEAT:
> > 25.91156
> > CYCLE: 23 TIME: 0.02 TIME LEFT: 3599.3 GRAD.: 13.892 HEAT:
> > 25.90275
> > CYCLE: 24 TIME: 0.02 TIME LEFT: 3599.2 GRAD.: 9.735 HEAT:
> > 25.81259
> > CYCLE: 25 TIME: 0.03 TIME LEFT: 3599.2 GRAD.: 7.760 HEAT:
> > 25.80691
> > HEAT OF FORMATION TEST SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 26 TIME: 0.02 TIME LEFT: 3599.2 GRAD.: 14.180 HEAT:
> > 25.80854
> > TEST ON X SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 27 TIME: 0.05 TIME LEFT: 3599.1 GRAD.: 12.093 HEAT:
> > 25.80834
> > CYCLE: 28 TIME: 0.04 TIME LEFT: 3599.1 GRAD.: 16.831 HEAT:
> > 26.51455
> > CYCLE: 29 TIME: 0.04 TIME LEFT: 3599.1 GRAD.: 11.681 HEAT:
> > 25.97852
> > CYCLE: 30 TIME: 0.02 TIME LEFT: 3599.0 GRAD.: 13.509 HEAT:
> > 25.83525
> > CYCLE: 31 TIME: 0.03 TIME LEFT: 3599.0 GRAD.: 15.172 HEAT:
> > 25.82875
> > CYCLE: 32 TIME: 0.02 TIME LEFT: 3599.0 GRAD.: 19.211 HEAT:
> > 25.81824
> > CYCLE: 33 TIME: 0.03 TIME LEFT: 3599.0 GRAD.: 18.735 HEAT:
> > 25.81237
> > HEAT OF FORMATION TEST SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 34 TIME: 0.05 TIME LEFT: 3598.9 GRAD.: 16.904 HEAT:
> > 25.81041
> > CYCLE: 35 TIME: 0.04 TIME LEFT: 3598.9 GRAD.: 5.983 HEAT:
> > 25.79806
> > CYCLE: 36 TIME: 0.02 TIME LEFT: 3598.8 GRAD.: 8.104 HEAT:
> > 25.79548
> > CYCLE: 37 TIME: 0.02 TIME LEFT: 3598.8 GRAD.: 7.677 HEAT:
> > 25.78943
> > HEAT OF FORMATION TEST SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 38 TIME: 0.02 TIME LEFT: 3598.8 GRAD.: 6.764 HEAT:
> > 25.78962
> > CYCLE: 39 TIME: 0.03 TIME LEFT: 3598.8 GRAD.: 3.953 HEAT:
> > 25.78183
> > CYCLE: 40 TIME: 0.02 TIME LEFT: 3598.7 GRAD.: 4.130 HEAT:
> > 25.77325
> > CYCLE: 41 TIME: 0.02 TIME LEFT: 3598.7 GRAD.: 3.516 HEAT:
> > 25.76796
> > CYCLE: 42 TIME: 0.02 TIME LEFT: 3598.7 GRAD.: 3.200 HEAT:
> > 25.76502
> > HEAT OF FORMATION TEST SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 43 TIME: 0.02 TIME LEFT: 3598.7 GRAD.: 2.985 HEAT:
> > 25.76321
> > HEAT OF FORMATION TEST SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 44 TIME: 0.02 TIME LEFT: 3598.7 GRAD.: 3.145 HEAT:
> > 25.76238
> > TEST ON X SATISFIED
> > HOWEVER, A COMPONENT OF GRADIENT IS LARGER THAN 0.20
> >
> > CYCLE: 45 TIME: 0.05 TIME LEFT: 3598.6 GRAD.: 5.357 HEAT:
> > 25.76203
> >
> >
> > HERBERTS TEST SATISFIED - GEOMETRY OPTIMIZED
> >
> >
> >
> -------------------------------------------------------------------------------
> > AM1 ANALYT MMOK GEO-OK PRECISE CHARGE=0
> > created by wmopcrt() for mopac
> >
> >
> >
> > HERBERTS TEST WAS SATISFIED IN BFGS
> > SCF FIELD WAS ACHIEVED
> >
> >
> > AM1 CALCULATION
> > VERSION 6.00
> >
> >
> >
> >
> >
> >
> > FINAL HEAT OF FORMATION = 25.76203 KCAL
> >
> >
> > TOTAL ENERGY = -1044.78567 EV
> > ELECTRONIC ENERGY = -4208.70236 EV
> > CORE-CORE REPULSION = 3163.91669 EV
> >
> > GRADIENT NORM = 5.35655
> > IONIZATION POTENTIAL = 8.43405
> > NO. OF FILLED LEVELS = 18
> > MOLECULAR WEIGHT = 110.173
> >
> >
> > SCF CALCULATIONS = 75
> > COMPUTATION TIME = 1.399 SECONDS
> >
> >
> >
> > FINAL POINT AND DERIVATIVES
> >
> > PARAMETER ATOM TYPE VALUE GRADIENT
> > 1 2 C BOND 1.390851 -0.168446
> > KCAL/ANGSTROM
> > 2 3 C BOND 1.401054 0.768599
> > KCAL/ANGSTROM
> > 3 3 C ANGLE 120.435448 4.078547
> > KCAL/RADIAN
> > 4 4 C BOND 1.395659 -0.827968
> > KCAL/ANGSTROM
> > 5 4 C ANGLE 119.999848 1.416238
> > KCAL/RADIAN
> > 6 4 C DIHEDRAL 0.020955 -0.147354
> > KCAL/RADIAN
> > 7 5 C BOND 1.398576 0.090437
> > KCAL/ANGSTROM
> > 8 5 C ANGLE 119.466655 2.697975
> > KCAL/RADIAN
> > 9 5 C DIHEDRAL -0.106678 -0.270464
> > KCAL/RADIAN
> > 10 6 C BOND 1.394512 -0.388200
> > KCAL/ANGSTROM
> > 11 6 C ANGLE 119.913535 -0.829211
> > KCAL/RADIAN
> > 12 6 C DIHEDRAL 360.147135 0.045847
> > KCAL/RADIAN
> > 13 7 H BOND 1.099642 -0.148975
> > KCAL/ANGSTROM
> > 14 7 H ANGLE 120.361455 0.010111
> > KCAL/RADIAN
> > 15 7 H DIHEDRAL 179.913600 -0.138768
> > KCAL/RADIAN
> > 16 8 S BOND 1.696534 -0.033882
> > KCAL/ANGSTROM
> > 17 8 S ANGLE 116.652987 -0.004508
> > KCAL/RADIAN
> > 18 8 S DIHEDRAL 180.038056 0.089590
> > KCAL/RADIAN
> > 19 9 H BOND 1.321621 0.015013
> > KCAL/ANGSTROM
> > 20 9 H ANGLE 100.024499 -0.014487
> > KCAL/RADIAN
> > 21 9 H DIHEDRAL 180.015929 0.001633
> > KCAL/RADIAN
> > 22 10 H BOND 1.100324 0.275908
> > KCAL/ANGSTROM
> > 23 10 H ANGLE 119.865018 -0.024151
> > KCAL/RADIAN
> > 24 10 H DIHEDRAL 180.009967 -0.005852
> > KCAL/RADIAN
> > 25 11 H BOND 1.100051 0.535439
> > KCAL/ANGSTROM
> > 26 11 H ANGLE 120.065829 -0.206468
> > KCAL/RADIAN
> > 27 11 H DIHEDRAL 179.880509 -0.125435
> > KCAL/RADIAN
> > 28 12 H BOND 1.100154 -0.010576
> > KCAL/ANGSTROM
> > 29 12 H ANGLE 119.668204 0.147048
> > KCAL/RADIAN
> > 30 12 H DIHEDRAL 179.839425 -0.079062
> > KCAL/RADIAN
> > 31 13 H BOND 1.101550 0.153800
> > KCAL/ANGSTROM
> > 32 13 H ANGLE 120.071170 -0.023569
> > KCAL/RADIAN
> > 33 13 H DIHEDRAL 179.968547 -0.000284
> > KCAL/RADIAN
> >
> >
> >
> >
> >
> > ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
> > NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
> > (I) NA:I NB:NA:I NC:NB:NA:I NA
> > NB NC
> >
> > 1 C
> > 2 C 1.39085 * 1
> > 3 C 1.40105 * 120.43545 * 1 2
> > 4 C 1.39566 * 119.99985 * 0.02095 * 2
> > 1 3
> > 5 C 1.39858 * 119.46666 * -0.10668 * 3
> > 1 2
> > 6 C 1.39451 * 119.91354 * 0.14713 * 5
> > 3 1
> > 7 H 1.09964 * 120.36145 * 179.91360 * 5
> > 3 1
> > 8 S 1.69653 * 116.65299 * -179.96194 * 3
> > 1 2
> > 9 H 1.32162 * 100.02450 * -179.98407 * 8
> > 3 1
> > 10 H 1.10032 * 119.86502 * -179.99003 * 2
> > 1 3
> > 11 H 1.10005 * 120.06583 * 179.88051 * 4
> > 2 1
> > 12 H 1.10015 * 119.66820 * 179.83942 * 6
> > 5 3
> > 13 H 1.10155 * 120.07117 * 179.96855 * 1
> > 2 3
> >
> >
> > INTERATOMIC DISTANCES
> > 0
> > C 1 C 2 C 3 C 4 C 5
> C
> > 6
> >
> >
> ------------------------------------------------------------------------------
> > C 1 0.000000
> > C 2 1.390851 0.000000
> > C 3 1.401054 2.423153 0.000000
> > C 4 2.413189 1.395659 2.798406 0.000000
> > C 5 2.418010 2.793659 1.398576 2.420758 0.000000
> > C 6 2.783235 2.413516 2.417832 1.394702 1.394512
> > 0.000000
> > H 7 3.419302 3.893267 2.172542 3.414246 1.099642
> > 2.162072
> > S 8 2.640776 3.948593 1.696534 4.492655 2.734893
> > 4.011218
> > H 9 3.612398 4.748102 2.324972 4.947194 2.709874
> > 4.104245
> > H 10 2.160860 1.100324 3.419005 2.168069 3.893978
> > 3.412755
> > H 11 3.410565 2.167102 3.898456 1.100051 3.417723
> > 2.167469
> > H 12 3.883388 3.411165 3.413543 2.164559 2.161890
> > 1.100154
> > H 13 1.101550 2.164086 2.167025 3.412778 3.414823
> > 3.884780
> > 0
> > H 7 S 8 H 9 H 10 H 11
> H
> > 12
> >
> >
> ------------------------------------------------------------------------------
> > H 7 0.000000
> > S 8 2.936343 0.000000
> > H 9 2.384988 1.321621 0.000000
> > H 10 4.993591 4.801124 5.727025 0.000000
> > H 11 4.320675 5.592453 6.021376 2.499188 0.000000
> > H 12 2.484300 4.895292 4.755528 4.321891 2.496159
> > 0.000000
> > H 13 4.327976 2.761270 3.974808 2.490726 4.321147
> > 4.984933
> > 0
> > H 13
> > ------------------
> > H 13 0.000000
> >
> >
> > EIGENVALUES
> >
> > -39.40742 -31.92992 -31.63795 -23.85487 -23.55291 -19.37608 -17.51380
> > -16.49351
> > -15.68651 -14.52706 -14.30778 -13.98590 -12.66171 -12.14265 -11.59784
> > -11.02347
> > -9.86160 -8.43405 0.20932 0.39515 0.69547 1.57364 2.71047
> > 3.77318
> > 3.83428 4.00490 4.28058 4.39683 4.72055 4.93894 5.17800
> > 5.35601
> > 5.53750 5.88166
> >
> >
> > NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
> >
> > ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY
> > 1 C -0.1189 4.1189
> > 2 C -0.1134 4.1134
> > 3 C -0.2102 4.2102
> > 4 C -0.1373 4.1373
> > 5 C -0.1450 4.1450
> > 6 C -0.1125 4.1125
> > 7 H 0.1303 0.8697
> > 8 S 0.1438 5.8562
> > 9 H 0.0192 0.9808
> > 10 H 0.1349 0.8651
> > 11 H 0.1336 0.8664
> > 12 H 0.1327 0.8673
> > 13 H 0.1428 0.8572
> > DIPOLE X Y Z TOTAL
> > POINT-CHG. -0.260 -0.265 0.000 0.371
> > HYBRID 0.962 1.253 -0.002 1.580
> > SUM 0.702 0.988 -0.002 1.212
> >
> >
> > CARTESIAN COORDINATES
> >
> > NO. ATOM X Y Z
> >
> > 1 C 0.0000 0.0000 0.0000
> > 2 C 1.3909 0.0000 0.0000
> > 3 C -0.7097 1.2080 0.0000
> > 4 C 2.0887 1.2087 0.0004
> > 5 C -0.0084 2.4180 0.0023
> > 6 C 1.3861 2.4135 0.0014
> > 7 H -0.5505 3.3747 0.0009
> > 8 S -2.4026 1.0961 0.0010
> > 9 H -2.7180 2.3795 0.0004
> > 10 H 1.9388 -0.9542 -0.0002
> > 11 H 3.1887 1.2099 0.0024
> > 12 H 1.9338 3.3677 0.0005
> > 13 H -0.5520 -0.9533 -0.0005
> >
> >
> > ATOMIC ORBITAL ELECTRON POPULATIONS
> >
> > 1.21495 0.93656 0.95828 1.00914 1.21749 0.93344 0.97464
> > 0.98781
> > 1.20948 0.97728 0.96841 1.05509 1.21867 0.99079 0.92067
> > 1.00715
> > 1.21690 0.94505 0.95010 1.03298 1.21733 0.93178 0.97511
> > 0.98825
> > 0.86966 1.85069 0.98322 1.10275 1.91958 0.98076 0.86506
> > 0.86642
> > 0.86732 0.85720
> >
> >
> >
> > TOTAL CPU TIME: 1.40 SECONDS
> >
> > == MOPAC DONE ==
> >
>
> Bill Ross, in regards to your last comment...
>
> > Note that csh is different from sh and bash, so scripts will have
> > to be re-written if switching to bash.
> >
> It seems some of the scripts are written in sh and some in csh. I have
> packages for both shells. I have been letting everything use its default
> shell that it was written in so I do not understand what you mean.
>
> In regards to Giorgio's post...
>
> > I think that the problem that you have found could be due to some
> > difference of the "sh" shell between ubuntu and RedHat based
> > distributions: in Ubuntu /bin/sh is a link to /bin/dash while in RedHat
> > is a link to /bin/bash. There are few differences between bash and dash,
> > but they are enough to raise some problems.
> >
> > In your case antechamber call $AMBERHOME/exe/mopac.sh and is this that
> > fail. One solution is to change the header of all the shell scripts in
> > the $AMBERHOME/exe folder from "#!/bin/sh" to "#!/bin/bash" (with out
> > quotation marks). You could type into a shell:
> >
> > sed -i -s 's|#!/bin/sh|#!/bin/bash|g' $AMBERHOME/exe/*
> >
> > This command will change all the headers and fix the problem.
> >
> > My best regards.
> > Giorgio Maccari.
> >
> I would like another confirmation that this is the issue before I make such
> a change. I also don't understand why the change would be made in the bin
> folder which the exe folder links to rather than somewhere in the src
> folder
> where the source code is.
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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