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
--
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
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Received on Tue Apr 28 2015 - 06:30:05 PDT
