Hi,
so you are saying that C1 and C2 are ca(=pure aromatic system) but C3
and C4 within the same aromatic ring should be cc=(non-pure aromatic
system)? C5 is in the 5-ring and that may be what is happening here:
6-ring pure aromatic, 5-ring not. You have to draw the line
somewhere. Of course, you can assign the atoms you think are more
suitable by hand or maybe even validate either set.
It is not immediately obvious why either choice would be better than
the other. But I guess that's one of the limits of strict atom
typing. You could individually parameterise all terms or just the
ones in question, and possibly catch the chemistry better.
Cheers,
Hannes.
On Tue, 28 Apr 2015 09:03:24 -0400
Robert Molt <rwmolt07.gmail.com> wrote:
> Good morning,
>
> I am saying that the two fusion points are both cc atoms, in terms of
> the GAFF atom types (or at leas they should be ). However, when you
> look at the table of atom types, there is only 1 cc-atom type.
>
> On 4/28/15 2:21 AM, hannes.loeffler.stfc.ac.uk wrote:
> > Hi,
> >
> > to understand how antechamber works is to first read the original
> > paper on it (I just don't have the reference here at the moment but
> > it must be cited in the manual) or best probably to read the source
> > code. If you run antechamber with -s 2 it tells what
> > "sub-programs" it is running (antechamber itself is mostly a driver
> > program). You would then see that the first one to run is bondtype
> > followed by atomtype.
> >
> > It is not clear to me, however, what your argument regarding the
> > atom types really is. If you consider the pyrimidine ring to be
> > aromatic then surely both C3 and C4 (the two fusion points) must be
> > the same, aromatic, atom type. You have drawn it that way
> > yourself.
> >
> > Cheers,
> > Hannes.
> >
> >
> > ________________________________________
> > From: Robert Molt [rwmolt07.gmail.com]
> > Sent: 28 April 2015 02:19
> > To: AMBER Mailing List
> > Subject: [AMBER] Antechamber Algorithm for Atom Type
> >
> > Good evening!
> >
> > I have a small, planar, aromatic organic molecule (C, N, H, O
> > atoms). I encountered a problem in parameterizing with GAFF; 4
> > dihedrals were not available. I tried to identify the four atoms in
> > the dihedral in my molecule, so I could just calculate the
> > torsional PES and add the parameters, and found some challenges. I
> > have attached a photo of the molecule in question.
> >
> > a.) Specifically, I was informed that I lacked 2 ca-ca-cc-h4
> > dihedral parameters and 2 ca-ca-cc-nd dihedral parameters by xleap.
> > However, when I look at the molecule, this designation does not
> > seem to make sense. There are 3 ca type carbons in the molecule, if
> > I understand properly, and none of them are adjacent to one
> > another; there is no cc adjacent to a h4. I /assume/, perhaps
> > erroneously, that the "best" choice in dihedrals to form will be
> > the ones that do not "jump" over atoms and thus go over grater
> > distances.
> >
> > b.) To confirm this, I examined ANTECHAMBER_AC.AC. It lists the
> > following table:
> >
> > ATOM 1 C1 MOL 1 -1.428 -1.191 -0.001
> > 0.000000 ca ATOM 2 N1 MOL 1 -2.039 0.009
> > 0.000 0.000000 nb ATOM 3 C2 MOL 1 -1.280
> > 1.097 -0.003 0.000000 ca ATOM 4 C3 MOL 1
> > 0.124 0.968 -0.003 0.000000 ca ATOM 5 C4 MOL
> > 1 0.596 -0.349 0.001 0.000000 ca ATOM 6 N2
> > MOL 1 -0.146 -1.465 0.002 0.000000 nb ATOM
> > 7 C5 MOL 1 1.299 1.764 -0.006 0.000000 cc
> > ATOM 8 H1 MOL 1 1.405 2.837 -0.014
> > 0.000000 h4 ATOM 9 N3 MOL 1 -1.900 2.297
> > -0.029 0.000000 nh ATOM 10 H2 MOL 1 -2.896
> > 2.310 0.100 0.000000 hn ATOM 11 H3 MOL 1
> > -1.380 3.137 0.142 0.000000 hn ATOM 12 N4 MOL
> > 1 2.371 1.010 -0.003 0.000000 nd ATOM 13 N5
> > MOL 1 1.942 -0.275 0.002 0.000000 na ATOM
> > 14 C6 MOL 1 2.878 -1.373 0.005 0.000000 c3
> > ATOM 15 H4 MOL 1 3.505 -1.324 0.893
> > 0.000000 h1 ATOM 16 H5 MOL 1 2.301 -2.294
> > 0.006 0.000000 h1 ATOM 17 H6 MOL 1 3.506
> > -1.327 -0.883 0.000000 h1 ATOM 18 O1 MOL 1
> > -2.253 -2.246 -0.001 0.000000 oh ATOM 19 H7 MOL
> > 1 -3.150 -1.895 -0.005 0.000000 ho
> >
> > To me, this seemingly confirms my suspicion in a.) This table lists
> > there to be 4 ca's in the molecule and one cc. However, pursuant to
> > the original GAFF paper, I would say that there are 3 ca's and 2
> > cc's in the molecule (by my eye). Either that or I deserve an F in
> > organic chemistry, and hopefully Dr. Farrell is not on this
> > list-serv.
> >
> > c.) I am wondering if the antechamber algorithm for designating
> > atom types is meeting a pathological case? i.e., that it is
> > assigning incorrect atom types? I would guess that antechamber
> > uses a distance-based criterion for designating atom types? I am
> > having trouble finding out in the manual how antechamber takes xyz
> > coordinates read in to decide atom types?
> >
> > --
> > Dr. Robert Molt Jr.
> > r.molt.chemical.physics.gmail.com
> > Nigel Richards Research Group
> > Department of Chemistry & Chemical Biology
> > Indiana University-Purdue University Indianapolis
> > LD 326
> > 402 N. Blackford St.
> > Indianapolis, IN 46202
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 28 2015 - 07:00:02 PDT
