AMBER Archive (2004)

Subject: AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in)

From: 吴磊 (wl_phy_at_163.com)
Date: Wed Jul 21 2004 - 05:59:13 CDT

But the connection information from column 5 to 7 seems to have used the atom numbers.

> On Sat, Jul 17, 2004, Wu Lei wrote:
> >
> > look at the last three atoms
> >
> > PHENYLALANINE, ALL ATOM AROMATIC PARAMETERS, COO- ANION
> > PHE
> > PHE INT 1
> > CORR OMIT DU BEG
> > 0.00
> > 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
> > 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
> > 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
> > 4 N N M 3 2 1 1.335 116.600 180.000 -0.57000
> > 5 HN H E 4 3 2 1.010 119.800 0.000 0.37000
> > 6 CA CH M 4 3 2 1.449 121.900 180.000 0.10000
> > 7 CB C2 S 6 4 3 1.525 111.100 60.000 0.11500
> > 8 CG CK S 7 6 4 1.510 115.000 180.000 -0.11500
> > 9 CD1 CK B 8 7 6 1.400 120.000 180.000 -0.11500
> > 10 HD1 HK E 9 8 7 1.090 120.000 0.000 0.11500
> > 11 CE1 CK B 9 8 7 1.400 120.000 180.000 -0.11500
> > 12 HE1 HK E 11 9 8 1.090 120.000 180.000 0.11500
> > 13 CZ CK B 11 9 8 1.400 120.000 0.000 -0.11500
> > 14 HZ HK E 13 11 9 1.090 120.000 180.000 0.11500
> > 15 CE2 CK B 13 11 9 1.400 120.000 0.000 -0.11500
> > 16 HE2 HK E 15 13 11 1.090 120.000 180.000 0.11500
> > 17 CD2 CK S 15 13 11 1.400 120.000 0.000 -0.11500
> > 18 HD2 HK E 17 15 13 1.090 120.000 180.000 0.11500
> > 14 (19?) C C M 6 4 3 1.522 111.100 180.000 0.70000
> > 15 (20?) O O2 E 14 6 4 1.229 120.500 0.000 -0.80000
> > 16 (21?) OXT O2 E 14 6 4 1.229 120.500 180.000 -0.80000
>
> The numbers in the first column are not used for anything, as far as I know.
>
> ...dac
>
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