AMBER Archive (2004)

Subject: Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Apr 20 2004 - 15:13:09 CDT

Dear Mr. Case,

I have the following gaussian input file:

----------------------------------------
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6)

remark line goes here

0 1
    C 1.0000 -7.6250 2.3110
    C 1.0000 -6.5910 3.6390
    C 1.0000 -7.8280 0.1950
    C 1.0000 -8.3580 0.1170
    C 1.0000 -5.3450 1.8010
    C 1.0000 -8.7370 1.5510
    C 1.0000 -4.3440 2.0550
    C 1.0000 -6.8540 -0.8950
    C 1.0000 -4.4840 3.1570
    H 1.0000 -3.4700 1.5820
    H 1.0000 -8.7580 1.8040
    H 1.0000 -8.5350 0.0740
    H 1.0000 -7.5970 -0.1630
    H 1.0000 -8.0170 3.2090
    H 1.0000 -5.3450 1.0650
    H 1.0000 -3.6100 4.1840
    H 1.0000 -2.8120 3.1350
    H 1.0000 -9.1220 -1.6860
    H 1.0000 -6.0860 -1.7300
    H 1.0000 -10.2970 1.3160
    H 1.0000 -7.4010 -1.8190
    H 1.0000 -6.2540 -0.5180
    N 1.0000 -5.5600 3.9460
    N 1.0000 -6.4690 2.5800
    N 1.0000 -3.5380 3.4640
    O 1.0000 -7.1830 1.4860
    O 1.0000 -7.6400 4.3120
    O 1.0000 -9.9910 1.9190
    O 1.0000 -9.4410 -0.7720
    O 1.0000 -5.8440 -1.1100
------------------------------------------

After using gaussian, I checked out the result in MOLDEN. The molecule is
on a 2-D surface, not in a 3-D. I do not understand why this happens. The
.pdb file I am using is either a cytosine or isocytosine taken from CCD
database. In any case, after using antechamber here is the .mol2 file and
the same structure placed on a 2-D surface is seen in this result too:

------------------------------------------
@<TRIPOS>MOLECULE
MOL test.no.opt.mol2
   30 47 1 0 0
SMALL
CHARGE FROM PDB

@<TRIPOS>ATOM
      1 C1 -0.9350 0.3910 0.0000 C 1 MOL
-0.4521
      2 C2 -1.6680 -1.1240 0.0000 C 1 MOL
0.9088
      3 C3 0.8720 1.5110 0.0000 C 1 MOL
1.3320
      4 C4 0.7070 2.0200 0.0000 C 1 MOL
0.0769
      5 C5 0.5320 -1.4270 0.0000 C 1 MOL
-0.2105
      6 C6 -0.7470 1.7250 0.0000 C 1 MOL
-0.9080
      7 C7 0.7480 -2.4370 0.0000 C 1 MOL
-0.3026
      8 C8 2.2800 1.1200 0.0000 C 1 MOL
-1.1053
      9 C9 -0.3020 -2.8000 0.0000 C 1 MOL
1.0332
     10 H1 1.5590 -3.0110 0.0000 H 1 MOL
0.1529
     11 H2 -0.9830 1.6320 0.0000 H 1 MOL
0.5425
     12 H3 0.6670 2.1980 0.0000 H 1 MOL
0.7428
     13 H4 1.2950 1.4620 0.0000 H 1 MOL
-1.5207
     14 H5 -1.9140 0.3450 0.0000 H 1 MOL
0.4594
     15 H6 1.1920 -1.1010 0.0000 H 1 MOL
0.2156
     16 H7 -0.8360 -4.0380 0.0000 H 1 MOL
0.2547
     17 H8 0.4580 -4.2890 0.0000 H 1 MOL
0.3925
     18 H9 1.9850 3.5040 0.0000 H 1 MOL
0.3868
     19 H10 3.3690 0.8020 0.0000 H 1 MOL
0.7151
     20 H11 -1.2270 3.2270 0.0000 H 1 MOL
0.5081
     21 H12 2.8660 2.0200 0.0000 H 1 MOL
0.2615
     22 H13 2.2080 0.4150 0.0000 H 1 MOL
0.8121
     23 N1 -1.4860 -2.1840 0.0000 N 1 MOL
-1.1815
     24 N2 -0.6640 -0.7640 0.0000 N 1 MOL
0.4025
     25 N3 -0.1580 -3.7840 0.0000 N 1 MOL
-0.6133
     26 O1 0.0000 0.3600 0.0000 O 1 MOL
0.0938
     27 O2 -2.7360 -0.4820 0.0000 O 1 MOL
-0.7706
     28 O3 -1.6320 2.6860 0.0000 O 1 MOL
-0.7158
     29 O4 1.0240 3.3850 0.0000 O 1 MOL
-0.8263
     30 O5 2.9210 0.3100 0.0000 O 1 MOL
-0.6846
@<TRIPOS>BOND
     1 1 2 1
     2 1 6 1
     3 1 11 1
     4 1 14 1
     5 1 24 1
     6 1 26 1
     7 2 23 1
     8 2 24 1
     9 2 27 1
    10 3 6 ar
    11 3 8 ar
    12 3 12 1
    13 3 26 ar
    14 3 29 ar
    15 4 6 ar
    16 4 8 ar
    17 4 13 1
    18 4 26 ar
    19 4 29 ar
    20 5 7 1
    21 5 9 ar
    22 5 15 1
    23 5 24 ar
    24 5 26 ar
    25 6 26 ar
    26 6 28 1
    27 7 9 1
    28 7 10 1
    29 7 25 1
    30 8 13 1
    31 8 19 1
    32 8 21 1
    33 8 22 1
    34 9 16 1
    35 9 23 ar
    36 9 25 1
    37 11 28 1
    38 12 29 1
    39 14 27 1
    40 16 25 1
    41 17 25 1
    42 18 29 1
    43 19 30 1
    44 20 28 1
    45 22 30 1
    46 23 24 ar
    47 24 26 ar
@<TRIPOS>SUBSTRUCTURE
     1 MOL 1 TEMP 0 **** **** 0 ROOT
-----------------------------------

Do you think that, maybe, the antechamber command -fo gcrt is creating a
structure which is too strange? I am open to any suggestion/procedure on
how to create the input file starting from a .pdb file. Thanks in
advance... 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       - Home Address:                -
  - University of Rochester      -                              -
  - Hutchison Hall, Office B10   - 60 Crittenden Blvd. Apt. 232 -
  - Rochester, NY 14627-0216     - Rochester, NY 14620          -
  - Ph.:(585) 275 20 31 (Office) - Ph.:(585) 242 91 37 (Home)   -
  - Homepage: http://www.pas.rochester.edu/~yildirim/           -
  ---------------------------------------------------------------

On Mon, 19 Apr 2004, David A. Case wrote:

> On Mon, Apr 19, 2004, Ilyas Yildirim wrote:
> >
> > #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
> >
> > but it gave the following error in the output
> > ---------------------------
> > ...
> >     30  O         nan        nan        nan        nan        nan
> >                    26         27         28         29         30
> >     26  O         nan
> >     27  O         nan        nan
> >     28  O         nan        nan        nan
> >     29  O         nan        nan        nan        nan
> >     30  O         nan        nan        nan        nan        nan
> >
> >  Error termination via Lnk1e in /opt/gaussian/g98/l202.exe.
>
> > I used molden to see how the structure looks like, but it does not look
> > like a normal structure.The atoms lay down on a plane which is wrong.
>
> If you have a bad initial structure, there is not much that either Gaussian
> or antechamber can do.  The "nan" above in the Gaussian output means "not a
> number", meaning that Gaussian totally failed to interpret your input data.
>
> Without seeing the input file, one cannot say why this is.  If you are using
> antechamber to create the input file, you still need to make sure that the
> Gaussian input makes sense.  Antechamber is sometimes bad at recognizing bad
> input data, and may go ahead and write a Gaussian input file even when it
> failed to correctly parse the input pdb file.  Again, it is hard to say when
> so little information is provided.
>
> >
> > 2. How can I modify the input command line so that I do not OPTIMIZE the
> > structure, but just get the ESP Data points?
>
> Remove the "opt" keyword from the Gaussian file.
>
> ...good luck...dac
>
>

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