Hi,
I am gradually making my way through all the obstacles with antechamber, and here is hopefully last one.
Without messing much with the C-code of am1bcc.c, like David did, I tried a phenol example with antechamber/am1bcc in the user-friendly way.
A very easy way to see what is going on is to give am1bcc an "ac" file with zero charges:
The file that is normally produced by antechamber ANTECHAMBER_AC.AC has exactly that:
CHARGE 0.00 ( 0 )
Formula: H6 C6 O1
ATOM 1 C1 POL 1 -0.949 -1.157 0.000 0.000000 ca
ATOM 2 C2 POL 1 0.445 -1.157 0.000 0.000000 ca
ATOM 3 C3 POL 1 1.127 0.068 0.000 0.000000 ca
ATOM 4 O4 POL 1 2.501 0.152 0.000 0.000000 oh
ATOM 5 C5 POL 1 0.425 1.285 0.000 0.000000 ca
ATOM 6 C6 POL 1 -0.966 1.260 0.000 0.000000 ca
ATOM 7 C7 POL 1 -1.655 0.045 0.000 0.000000 ca
ATOM 8 H8 POL 1 -1.492 -2.114 0.000 0.000000 ha
ATOM 9 H9 POL 1 1.003 -2.103 0.000 0.000000 ha
ATOM 10 H10 POL 1 2.854 -0.749 0.000 0.000000 ho
ATOM 11 H11 POL 1 0.982 2.232 0.000 0.000000 ha
ATOM 12 H12 POL 1 -1.525 2.207 0.000 0.000000 ha
ATOM 13 H13 POL 1 -2.754 0.038 0.000 0.000000 ha
BOND 1 1 2 7 C1 C2
BOND 2 1 7 8 C1 C7
BOND 3 1 8 1 C1 H8
BOND 4 2 3 8 C2 C3
BOND 5 2 9 1 C2 H9
BOND 6 3 4 1 C3 O4
BOND 7 3 5 7 C3 C5
BOND 8 4 10 1 O4 H10
BOND 9 5 6 8 C5 C6
BOND 10 5 11 1 C5 H11
BOND 11 6 7 7 C6 C7
BOND 12 6 12 1 C6 H12
BOND 13 7 13 1 C7 H13
Now I run am1bcc like this:
am1bcc -i ANTECHAMBER_AC.AC -o ANTECHAMBER_0AM1BCC.AC -f ac -p amber10/dat/antechamber/BCCPARM.DAT -s 2 -j 1
When I inspect the output "ac" file I only see three atoms got corrections and those involve the C-O-H fragment, so only two bonds.
I wonder what happened to C-H bonds? Are AM1 charges on the rest of the ring that good in this case that they do not require corrections to reproduce HF/6-31G*???
I tend to doubt that. Could you please help me understand.
Here is the output:
CHARGE 0.00 ( 0 )
Formula: H6 C6 O1
ATOM 1 C1 POL 1 -0.949 -1.157 0.000 0.000000 16
ATOM 2 C2 POL 1 0.445 -1.157 0.000 0.000000 16
ATOM 3 C3 POL 1 1.127 0.067 0.000 0.045100 16
ATOM 4 O4 POL 1 2.501 0.152 0.000 -0.246100 31
ATOM 5 C5 POL 1 0.426 1.285 0.000 0.000000 16
ATOM 6 C6 POL 1 -0.965 1.260 0.000 0.000000 16
ATOM 7 C7 POL 1 -1.654 0.045 0.000 0.000000 16
ATOM 8 H8 POL 1 -1.492 -2.114 0.000 0.000000 91
ATOM 9 H9 POL 1 1.003 -2.104 0.000 0.000000 91
ATOM 10 H10 POL 1 2.855 -0.750 0.000 0.201000 91
ATOM 11 H11 POL 1 0.983 2.232 0.000 0.000000 91
ATOM 12 H12 POL 1 -1.525 2.207 0.000 0.000000 91
ATOM 13 H13 POL 1 -2.753 0.037 0.000 0.000000 91
BOND 1 1 2 7 C1 C2
BOND 2 1 7 8 C1 C7
BOND 3 1 8 1 C1 H8
BOND 4 2 3 8 C2 C3
BOND 5 2 9 1 C2 H9
BOND 6 3 4 1 C3 O4
BOND 7 3 5 7 C3 C5
BOND 8 4 10 1 O4 H10
BOND 9 5 6 8 C5 C6
BOND 10 5 11 1 C5 H11
BOND 11 6 7 7 C6 C7
BOND 12 6 12 1 C6 H12
BOND 13 7 13 1 C7 H13
Thank you for your help,
-Ilja
On 8/7/09 7:54 PM, "case" <case.biomaps.rutgers.edu> wrote:
On Fri, Aug 07, 2009, David Mobley wrote:
>
> I am attaching just one example of profound disagreement. The 2-
> nitrothiophene.mol2 file contains Bayly AM1-BCC partial charges (sybyl
> atom naming); 2-nitrothiophene_ante_amber.mol2 contains antechamber
> AM1-BCC partial charges (amber atom naming), and 2-
> nitrothiophene_oechem_amber.mol2 contains OpenEye AM1-BCC partial
> charges.
David:
Thanks for sending the example. Let's look at the nitrogen charge you
mention:
>
> In this example, the Antechamber AM1-BCC charges differ from the
> others by more than 0.3 e on the nitrogen alone.
There are two possible origins for this. First, the AM1 Mulliken charge
might be different. We get 0.613 for the nitrogen Mulliken charge. I don't
know what the other programs give, but that would be interesting to check.
(For completeness, our minimized AM1 energy is 31.74.)
Second, and more likely, is that the BCC corrections are the source of
the difference. Here are the corrections that Junmei's am1bcc program
provides:
bond at1 at2 pre-charge correction post-charge
0 C1 N1 -0.4880 0.6130 -0.0452 -0.5332 0.6582
1 C1 C2 -0.5332 -0.0680 0.0000 -0.5332 -0.0680
2 C1 S1 -0.5332 0.7320 0.2699 -0.2633 0.4621
3 N1 O1 0.6582 -0.3680 0.0000 0.6582 -0.3680
4 N1 O2 0.6582 -0.3480 0.0000 0.6582 -0.3480
5 C2 C3 -0.0680 -0.1690 0.0000 -0.0680 -0.1690
6 C2 H1 -0.0680 0.1850 0.0000 -0.0680 0.1850
7 C4 S1 -0.4420 0.4621 0.2699 -0.1721 0.1922
8 C3 C4 -0.1690 -0.1721 0.0000 -0.1690 -0.1721
9 C3 H2 -0.1690 0.1680 0.0000 -0.1690 0.1680
10 C4 H3 -0.1721 0.1850 0.0000 -0.1721 0.1850
Note that there is only a small correction (from the C1-N1 bond). We don't
apply any corrections for the N1-O1 or the N1-O2 bond -- that seems a little
odd(??), and may indicate that there is a difference between our table of BCC
corrections and those that Chris or openeye are using.
Of course, at this point, I should (and will!) go check the above bond
corrections against the original papers. But I'm travelling right now,
without access to the needed papers. So maybe Junmei or someone on the list
can continue this check.
[as an aside: you can get the bond correction output above by setting the
"debug" flag in am1bcc.c. I've attached a patch file against the current
release that creates the above format, which is more readable than what is
there now....]
....regards...dac
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Received on Fri Aug 21 2009 - 10:11:12 PDT
