Re: [AMBER] R.E.D. double bond revisit

From: FyD <>
Date: Wed, 25 Sep 2013 22:40:33 +0200

Dear Henry,

> If we prepare RESP charges for a molecule with aromatic rings using the
> following steps:
> 1. Transfer a pdb file into a P2N file. (Scaling factor 1.2, Correct
> only redudant atom names , do not modify the atom order, root of the atom
> connectivities = 1, 0.0 means a single residue

So you use R.E.D. Server/Ante_R.E.D. 2.0, and not Ante_R.E.D. 1.x from
the R.E.D. tools III.x

> 2. The generated P2N doesn't seem to include any double bond atom types
> /aromatic connectivity from the original pdb file.

You are correct - no double bond is defined in the P2N file; no need
to do so when one targets FF development.

> 3. The following RESP charge determination using RESP-A1A and
> Gaussian 09 will generate a mol2 file. This mol2 will not have any "ar"
> symbol, which represents the C=C bond in a benzyl ring. If we use this
> mol2 file to generate .OFF, .frcmod & .prmtop and use acdoctor in
> AmberTools to check this generated .prmtop file, it will say "error:
> this .prmtop file has an open valance charge at the carbon atoms in the
> benzyl ring.

You are correct again. R.E.D. III.x and R.E.D. Server/R.E.D. IV (perl
versions) only reports simple bonds in mol2 files because in an
empirical FF a double or triple bond is simply represented by a
different FF constant.

R.E.D. perl versions does not perform atom typing...

It is possible that the Antechamber tools perform atom typing by using
the notion of simple/double and triple bonds. I do not know (we do not
use and do not support Antechamber); this is _not_ our approach in
R.E.D. Python. Concerning "acdoctor": I never used it: If I read the
manual of the AmberTools 13 page 152 about acdoctor - it looks like
this tool work on FF libraries; but not on a prmtop file: For me and
once again a prmtop file does not contain any information about
simple, double or triple bond, but only FF constants, which are more
or less important (and consequently indirectly reflect the notion of
simple, double and triple bonds)....

R.E.D. Python (1st released through R.E.D. Server Development soon)
does perform atom typing, but again does _not_ use double and triple
bonds. No need to do so for our algorithm.

> So from the previous posts
> <> (still
> confused after reading the tutorials and the previous try to
> clarify it here....) , it seems like even there is no double bond related
> atom type in P2N file, the "aromaticity is still included in RESP charge
> calculation. In Xleap, one can simply add double bond/change aromatic
> related atom types of benzyl ring in the mol2 file generated from R.E.D.
> server, and use this edited mol2 file to generate the .prmtop?

In LEaP, Yes, double and triple bonds can be constructed in the "Draw"
mode, but from what I understand this is only useful to add the right
number of hydrogen atoms and to relax a structure to get the right
hybridization (sp, sp2 or sp3)...

> Hope the post is not too confusing.... If yes, I am more than happy to
> re-describe it.

are you sure you used acdoctor on a prmtop file, and not on a mol2 file?

finally if one wants to use of a mol2 file to display the double and
triple bonds of a molecule in a graphical program the corresponding
information has obviously to be present in the file; R.E.D. generates
mol2 files, which are used as FF libraries; in this case the goal is
slightly different...

let me know if something is not clear...

regards, Francois

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Received on Wed Sep 25 2013 - 14:00:02 PDT
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