AMBER Archive (2004)

Subject: Re: AMBER: reproduction of RESP charges for Gly

From: FyD (
Date: Tue May 04 2004 - 15:16:00 CDT

Dear Mikyung Seo,

> I found that charges for Gly in all_amino94.lib (Amber7.0) are same as
> charges
> in Ref. P.Cieplak et al, JCP, 16, 1357 (1995).
> I tried to reproduce RESP charges for Gly using R.E.D and antechamber
> program(in version 7).
> First of all, I used the coordinates for Gly from all_amino94.lib and
> did
> single point energy calculation using Gaussian98. (I think all
> geometries in all_amino94.lib are already optimized)

What I would do is to use the starting coordinates you got from ... as a
starting point for minimization and NOT for single point (SP). Indeed, I see at
least two reasons why you could observed charge differences with the values
available in the xleap OFF libraries...

1- I wonder the number of digits after the decimal point you used in your SP
input: if you started from a PDB file (that has only three digits) some small
charge diff. may be observed; It is why the PDB files generated by R.E.D. have
four digits (The Tripos format generated by RED version 2.0 will present 6

2- I guess you generated a "Standard orientation" within your SP (I mean in the
Gaussian output). However, it is unlikely (depending on your model) that you
will get the same Standard orientation than the one generated when RESP charges
where calculated in 1994-1995. Thus, if 'your' minimum molecular orientation
used to compute the MEP is different from the one calculated in 1994-1995, the
RESP charges will be different. The charge differences induced by 2 different
molecular orientations are un-predictable and can display some noticeable (and
highly disturbing) differences... It is the main reason why we wrote R.E.D.

> After this I got charges for Gly but they are pretty different from
> charges in all_amino94.lib.
> Why are they so different? They used two Gly conformations for RESP
> charge-fitting in reference. What does this mean?

See above

> That means I can't use the coordinates for Gly in all_amino94.lib to
> reproduce charges?

This simply means that it is very unlikely you will be able to reproduce the
same RESP charge values than those published in 1995. The diff. observed might
or might not be disturbing (depending on the model and/or orientation).

> Second problem is that I also tried to use R.E.D to get resp charges.
> When I used gaussian output after single point energy calculation it
> gives "Invalid Minimization OUTPUT !" error message.

You need to use a GAMESS or Gaussian MINIMIZATION output as input in R.E.D. If
you load a SP output, you will get such messages... It is explained in the
R.E.D. manual.

> Can't R.E.D read gaussian output from single point energy calculation?


> How can I modify the code in this case?
> Is there any clear example to reproduce RESP charges? Are there any
> source of geometry and method to reprocude RESP charges?

So far, the ONLY way to derive reproducible RESP charges in to use the
rigid-body re-orientation algo. available in R.E.D. and to publish the RESP
charges with the orientation(s) selected. You can also apply multi-orientation
RESP fit to average the charge diff. observed for one orientation over several
orientations... In this case, the charges are reproducible whatever the ab
initio software used, i.e. using GAMESS or Gaussian...

Best regards, Francois

I think you can found similar explanations from the links I provided you in your
previous email.
See also the R.E.D. manual...

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
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