Hello,
The definitions of the terms may be an issue here, for me. You describe
cc as "non-pure aromatic system." I do not know what that means? In the
original GAFF paper, it describes it as "inner sp2 carbon on conjugated
ring systems." I assume that means the fusion points (the "inner" part)
on these conjugated rings, and hence there have to be exactly two.
Regardless, if the system is sufficiently non-canonical that either
a.) antechamber's specific atom designation subroutine called makes a
"mistake" in designation
b.) antechamber's specific atom designation subroutine does NOT make a
mistake and parameters are missing
then I should perhaps parameterize this on my own.
On 4/28/15 9:29 AM, Hannes Loeffler wrote:
> 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
>
> _______________________________________________
> 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 - 07:00:04 PDT
