AMBER Archive (2004)

Subject: AMBER: About RESP Calculation

From: Ilyas Yildirim (
Date: Fri Mar 19 2004 - 01:20:16 CST

Hi Amber Members,

I have a couple of question about RESP calculation. I found the .pdb
file of a Cytosine molecule in Cambridge Crystalographic Database,
CYTIDI10. I want to find the RESP charges of this particular molecule and
have a couple of questions to ask:

1. I have tried to use the program RED written by Mr. Dupradeau. I entered
the .pdb file and it took 3 days and still didnt end up with the
calculation. I killed the job. Are the gaussian calculations taking
that long? I did not change the ATOM NAMES, and later I realized that in
the sugar molecule, there is a CH2 term. Is it possible that this is the
reason for this problem? (If it is a problem for the gaussian to calculate
a particular job more than 3 days)

2. Do we have to optimize the structure of a particular molecule in order
to calculate the RESP charges? For instance, can I just use the crystal
structure I got from the CCD and just do the MEP calculation and then the
RESP calculations? Is this legitimate?

3. In the RED program, it is talking about re-orientation. I followed the
manual, and did not understand exactly what it is meant by reorientation.
In the tutorials there are examples for re-orientation, but after getting
an optimized structure, why do we have to reorient the structure? The
structure has a clear structure when viewed in InsightII or Molden. So,
isnt it legitimate to do the MEP calculation in Gaussian and then the RESP
calculations without reorient the structure?

4. I tried to follow Cornell's paper to recalculate the results published
in 1995. I read the RESP documents that are in the scripps website, and in
those info files it is saying that in order the results to be compatible
with Cornell et al. 95 force field,
  #P MP2/6-31G* pop=mk iop(6/33=2)
needs to be used in the gaussian input file. I use one of the cytosine
molecule used in Cornell et al. 95 paper. The gaussian gives an error
while doing the calculations. I do not exactly remember what the error
sentence is, but it needs more space in the harddrive, more than 20 Gbyte
space. Is this normal? It happened to me twice. I used
  #P HF/6-31G* pop=mk iop(6/33=2) SCF(Conver=6) Nosymm Test
which I found in Mr. Dubradeau's RED program manual, and it gives me a
result without any error.
PS: The above Gaussian command was described in an email sent by Jim
Caldwell to in Feb 21, 1996 with a subject "esp to

Thanks in advance.


  Ilyas Yildirim
  - Department of Chemisty       - Home Address:                -
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