Re: AMBER: Which program to use to visualize the RESP Outputs

From: Ilyas Yildirim <>
Date: Tue, 27 Jan 2004 13:49:01 -0500 (EST)

  Dear François,
  Thanks for your comments. I could see the charges in Insight 2 at last.
Thanks giving me the properties that needed to be adjusted.
  I have posted the problem to the AMBER list too. As you said, there are
a lot of ***** MEP points, and that might create this whole trouble.
  Best regards,

> Dear Ilyas,
>> Thanks for your response. I have converted the file to a .mol2 file,
>> and tried to look at the molecule using
> I do not think VMD can display charges...
>> and Insight II, but could not
> In InsightII:
> Molecule/Label
> Label Option = Single property
> Label level = Atom
> Label_action = on
> Molecule Spec = 'Your molecule'
> Label property = Partial_charge
> => charges are displayed with 2 digits.
> To display charges with four digits:
> Session/Environment
> Toggle 'Precicion' to 'on'
> Precision = '4' instead of '2'
> => charges are displayed with 4 digits i.e. as in the AMBER 'prep'
> files...
>> see the charges in these programs. I will try to check the file using
>> some other programs, like Maestro and MacroModel.
>> The main reason why I am writing to you is to ask a specific
>> question
>> about RESP Charge calculation. I am trying to recalculate the results
>> done in Cornell et.all 1995 paper, specifically for the Guanine and
>> Cytosine bases, with different sugar molecules attached to these
>> bases.
> You will NOT be able to reproduce the published values! It is why we wrote
> to be able to get (highly)
> reproducible
> RESP/ESP charges whatever is the ab-initio software is (GAMESS or Gaussian
> as
> examples) and whatever is the starting structure representing the target
> minimum...
>> 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 charges.
>> 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)
> From our tests SCF=Tight is NOT usefull. Only the 'accuracy' (Opt=Tight or
> even
> VTight) of the optimized structure is important... SCF=Tight in single
> point
> calculation does not affect the MEP.
> Moreover, it is explained at
> "IOp(6/33=2) makes Gaussian write out the potential points and potentials
> (do
> not change). IOp(6/41=10) specifies that 10 concentric layers of points
> are used
> for each atom (do not change). IOp(6/42) givest the density of points in
> each
> layer. A value of 17 gives about 2500 points/atom. Lower values may be
> needed
> for large molecules, since the programs cannot normally handle more than
> 100 000
> potential points. A value of 10 gives about 1000 points/atom."
> I ran a small calculation on MeOH using Iop(6/33=2, 6/41=10, 6/42=17) or
> Iop(6/33=2) and the number of MEP point is totally different with
> Iop(6/33=2,
> 6/41=10, 6/42=17) (a huge number of MEP points is reported). I do not
> think that
> this corresponds to the Connolly surface reported by Kollman and Singh. I
> would
> only use what is recommended on the AMBER web site i.e. 'only'
> Iop(6/33=2) (see
> "handy script/program to
> convert
> g94 output")
>> I got this command in one of the pages in internet. A prof. in Sweden,
>> Prof. Ulf Ryde, was using this method while calculating the RESP
>> charges. So, 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. all 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
> I think Prof. Ulf Ryde compared different ways to get ESP charges (not
> only RESP
> charges)...
>> I checked out the file you have written, and there, you are
>> using the following command while doing the MEP Calculation:
>> #P HF/6-31G* Pop=MK SCF(Conver=6) Iop(6/33=2) NoSymm Test
> We simply used what is reported on the AMBER web site adding. 'NoSymm' can
> be
> added to keep the orientation selected by the rigid body re-orientation
> algorithm available in RED...
>> What might be the problem that I am encountering while following my
>> procedure? In Cornell's paper, 4 surfaces need to be defined to
>> calculate the RESP charges, and I thought that Iop(...) is giving this
>> definitions.
> oh oh, 4 surfaces ? I do not follow you...
>> Then I have changed the first command of the g98 file with the way
>> of
>> yours, and did the same thing: First found the ESP fit points, and
>> then
>> used antechamber. I did not have any error messages in this case, and
>> got the RESP Charges. When I compared with the Cornell et. all 95
>> results, some of the charges were not close to the results of the
>> paper.
> I am not surprised: you can not reproduce published data. It is why we
> wrote RED
> . For the Cornell et al. paper, the charges have been calculated with
> Gaussian.
> As the orientation of the optimized structure obtained from GAMESS and
> Gaussian
> are different, you will not be able to reproduce the published values if
> you use
> GAMESS... Now if you have the money to use Gaussian ;-) I am sure that the
> orientation of the optimized structure you obtained is different from the
> orientation of the optimized structures obtained in the Cornell et al
> paper
> (even if you do use the default keyword 'Symmetry')... As the orientation
> are
> different, the charges are different and the differences can be quite
> important... See RED manual page 13... I am writting the RED paper...
>> I would love to hear what you think might be the reason why my first
>> method did not work. Thanks in advance.
> In the MeOH test I ran with Iop(6/33=2, 6/41=10, 6/42=17), there are so
> much MEP
> points that their numbers are replaced by "*****" at the end of the g98
> output.
> A reason could be that 'Antechamber' does not like such characters, I do
> not know...
> Best regards, Francois
> F.-Y. Dupradeau
> --
> The Scripps Research Institute, San Diego, CA
> Faculte de Pharmacie, UPJV, Amiens, France
> --
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Ilyas Yildirim
Department of Physics and Astronomy
University of Rochester

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Received on Tue Jan 27 2004 - 18:53:17 PST
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