AMBER Archive (2004)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Apr 19 2004 - 15:35:45 CDT

Hi Amberlist members,

I asked this question before, but did not get any answer yet. Let us say
that we have a crystal structure from pdb.org or from Cambridge
Crystallografic Database and let us say that this is just a nucleotide.
And we want to find the ESP Data points, namely we want to do MEP
calculations using Gaussian 98, and use the results in AMBER to get the
RESP charges. Is this possible to do? I am using the following command in
the gaussian input file (PS: I got this command from antechamber while
converting the pdb file into a gaussian input file)

#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
 This structure is nearly, but not quite of a higher symmetry.
 Consider Symm=Loose if the higher symmetry is desired.
 Stoichiometry C9H13N3O5
 Framework group C1[X(C9H13N3O5)]
 Deg. of freedom 84
 Full point group C1 NOp 1
 Omega: Change in point group or standard orientation.

 Error termination via Lnk1e in /opt/gaussian/g98/l202.exe.
 Job cpu time: 1 days 1 hours 28 minutes 54.0 seconds.
 File lengths (MBytes): RWF= 50 Int= 0 D2E= 0 Chk= 9 Scr= 1

---------------------------
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. It
seems that gaussian is trying to optimize the structure. My first question
is

1. How can I modify the input command line so that I can follow the
procedure described in Amber 7 Manual, pp. 259?
PS: I used

    $ antechamber -i <inputfile>.pdb -fi pdb -o <outputfile>.com -fo gcrt

to create the Gaussian input file.

2. How can I modify the input command line so that I do not OPTIMIZE the
structure, but just get the ESP Data points?

3. Is it possible to use ANTECHAMBER if I know the ESP Data points for a
particular structure?

PS: I know that it should be possible, but I have done some MEP
calculations and I could not use ANTECHAMBER. I am assuming that the
gaussian input command I used to do MEP calculations was the reason.
Therefore, the 2nd question above is my main concern.

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          -
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