AMBER Archive (2004)

Subject: AMBER: Error message in antechamber

From: Ilyas Yildirim (
Date: Tue Jan 27 2004 - 12:44:26 CST

  I am trying to recalculate the results done in Cornell et al. 1995
paper, specifically for the Guanine and Cytosine bases, with different
sugar molecules attached to these bases. I have modeled a Cytosine with
a sugar molecule attached to it, similar to the one done in Cornell
et.all 1995 (For the RNA Case). The molecule is in Fig. 6 on that paper.
The next step was to find the RESP Charges for this molecule. So, I am
using first g98 to get the ESP fit and then antechamber to get the RESP
  Before using the Gaussian, I changed the first line of the input file with

  #P HF/6-31G* SCF=Tight Pop=MK Iop(6/33=2, 6/41=10, 6/42=17)

  After getting the g98 output file, I used the antechamber with the
following command:

  antechamber -i <input file> -fi gout -o resp.prep -fo prepi -c resp -s 2

  When I used this procedure for a Cytosine with only Hydrogen atom
attached to the base, rather a sugar molecule, it worked fine, and I got
the RESP charges. But when I have a sugar molecule similar to the one
that is used in Cornell et al. 1995, it failed, and the following error
message came out while using antechamber:

  Running: resp -O -i ..... -------->The Resp1 calculation
  fmt: end of file
  apparent state: unit 10 named ANTECHAMBER.ESP
  last format: (2i5)
  lately reading sequential formatted external IO
  resp -O -i ..... ----------------->The Resp2 calculation
  Unit 3 error on OPEN: gout
  Cannot open QOUT, exit

  The Gaussian output file of the C-molecule with a sugar attached has a
lot of ***** MEP points in it. Can it be the reason why I am getting the
above error message while using antechamber? If it is, is there any way
of solving the problem without changing the first line in the gaussian
input file? Thanks in advance...

Ilyas Yildirim
Department of Physics and Astronomy
University of Rochester

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