Matt,
The AM1-BCC method was parameterized using AM1 charges from geom. optimized
molecules using the EF keyword in Mopac6. Therefore, in order to obtain
"correct" AM1-BCC charges, the BCC parameters should be used with geom.
optimized AM1 charges.
Also, these structures should not contain any intra-molecular H-bonds
because that will affect the AM1 charges.
I hope this helps,
Araz
****************************
Araz Jakalian, Ph.D.
Research Scientist, Structural Research Group
Boehringer Ingelheim (Canada) Ltd.
Research and Development
2100 Rue Cunard
Laval, Quebec, H7S 2G5, Canada
Phone: (450) 682-4640 Fax: (450) 682-4189
E-mail: ajakalian_at_lav.boehringer-ingelheim.com
****************************
> -----Original Message-----
> From: Matthew Lee [SMTP:mrlee_at_cgl.ucsf.edu]
> Sent: Tuesday, July 30, 2002 1:32 PM
> To: amber_at_heimdal.compchem.ucsf.edu
> Subject: AM1-BCC sensitivity to AM1 charges
>
> Hi--
>
> I am wondering if anyone has analyzed the sensitivity of
> correlation between AM1-BCC charges and RESP charges to single point
> AM1 vs. AM1 after geometry optimization. It seems the two approaches
> for AM1 charges differ, on average, by about 10% and 0.01 charge units
> on a small set of small molecules I've looked at.
>
> For comparison, on these same small molecules, the BCC alters
> the charges, on average, by about 60% and 0.07 charge units.
>
> Incidentally, the way to use sybyl's mopac is rather unusual
> in that it will not run unless there are 3 arguments after the STDOUT
> redirect. There was some questions on this reflector awhile back
> about this and I don't think a response was ever posted. The
> following mopac.sh works with the Sybyl distribution of mopac:
> --------------
> /home/tripos/sybyl6.7/bin/mopac < $1 > $2 junk.arc junk.syb
> /usr/bin/rm -f junk.arc junk.syb
> --------------
>
> To elaborate more on my concern, here is an example of the AM1
> charge differences I see between single point and geometry
> optimazation approaches on Raloxifene:
>
> Single Geom. Absol %
> ATOM Point Optimiz Change Change
> C1 -0.1591 -0.1365 0.0226 14.2
> C2 -0.1688 -0.2471 0.0783 46.4
> C3 -0.0931 -0.0824 0.0107 11.5
> C4 0.3323 0.3401 0.0078 2.3
> C5 -0.0624 -0.0709 0.0085 13.6
> S6 0.3472 0.5077 0.1605 46.2
> C7 -0.1854 -0.2752 0.0898 48.4
> C8 -0.0439 -0.0498 0.0059 13.5
> C9 -0.1967 -0.1924 0.0043 2.2
> O10 -0.2887 -0.2909 0.0022 0.8
> C11 -0.0626 -0.0698 0.0072 11.6
> C12 -0.0643 -0.0757 0.0114 17.7
> C13 -0.1297 -0.1329 0.0032 2.5
> C14 -0.2205 -0.2055 0.0150 6.8
> C15 -0.0331 -0.0415 0.0084 25.4
> C16 -0.0372 -0.0393 0.0021 5.5
> C17 -0.1591 -0.1566 0.0025 1.6
> C18 -0.2289 -0.2171 0.0118 5.2
> C19 0.1071 0.0870 0.0201 18.8
> C20 -0.1769 -0.1751 0.0018 1.0
> C21 -0.2499 -0.2303 0.0196 7.8
> C22 0.1063 0.0901 0.0162 15.3
> O23 -0.2464 -0.2501 0.0037 1.5
> C24 0.1066 0.1133 0.0067 6.3
> O25 -0.2478 -0.2477 0.0001 0.1
> O26 -0.1545 -0.1917 0.0372 24.1
> C27 -0.0394 -0.0271 0.0123 31.2
> C28 -0.1061 -0.0644 0.0417 39.3
> N29 -0.1812 -0.2465 0.0653 36.0
> C30 -0.1002 -0.0656 0.0346 34.6
> C31 -0.1081 -0.0691 0.0390 36.0
> C32 -0.1557 -0.1557 0.0000 0.0
> C33 -0.1551 -0.1555 0.0004 0.3
> C34 -0.1621 -0.1578 0.0043 2.7
> H35 0.1416 0.1475 0.0059 4.2
> H36 0.1585 0.1590 0.0005 0.3
> H37 0.1381 0.1373 0.0008 0.6
> H38 0.1534 0.1572 0.0038 2.5
> H39 0.1335 0.1373 0.0038 2.9
> H40 0.1544 0.1561 0.0017 1.1
> H41 0.1421 0.1454 0.0033 2.3
> H42 0.1517 0.1561 0.0044 2.9
> H43 0.1325 0.1355 0.0030 2.3
> H44 0.1503 0.1570 0.0067 4.4
> H45 0.1422 0.1391 0.0031 2.2
> H46 0.2270 0.2202 0.0068 3.0
> H47 0.2248 0.2190 0.0058 2.6
> H48 0.0834 0.0813 0.0021 2.6
> H49 0.0881 0.0848 0.0033 3.7
> H50 0.1099 0.1086 0.0013 1.2
> H51 0.0686 0.0585 0.0101 14.7
> H52 0.0940 0.0887 0.0053 5.7
> H53 0.0550 0.0470 0.0080 14.6
> H54 0.0540 0.0441 0.0099 18.3
> H55 0.0955 0.0927 0.0028 2.9
> H56 0.0993 0.0942 0.0051 5.1
> H57 0.0805 0.0818 0.0013 1.6
> H58 0.0798 0.0807 0.0009 1.1
> H59 0.1000 0.0943 0.0057 5.7
> H60 0.0835 0.0823 0.0012 1.5
> H61 0.0759 0.0764 0.0005 0.7
>
>
> Sincerely,
> --Matt
>
> *******************************************************************
> Matthew Randolph Lee, Ph.D.
>
> Computational Scientist phone: (858)410-6534
> Lion Bioscience Inc. fax: (858)410-6665
> 9880 Campus Point Drive e-mail: matthew.lee_at_lionbioscience.com
> San Diego, CA 92121
> *******************************************************************
Received on Tue Jul 30 2002 - 11:28:25 PDT
