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/631G* 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 146270216  Rochester, NY 14620 
 Ph.:(585) 275 20 31 (Office)  Ph.:(585) 242 91 37 (Home) 
 Homepage: http://www.pas.rochester.edu/~yildirim/ 


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