AMBER Archive (2004)

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

From: FyD (
Date: Tue Jan 27 2004 - 10:59:51 CST

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:
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:
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 RED 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

> 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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