From: li (zlee_at_ustc.edu)
Date: Sun Nov 14 2004 - 02:45:43 CST
> Replyed From: li <zlee_at_ustc.edu>
> Hi,andy:
> Here is what you need:
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node21.html
>
> good luck!
>
> > Dear Li,
> >
> > If you can, please explain some of these to me? I number each line for convenient.
> >
> > 01RESI ALA 0.00
> > 02GROUP
> > 03ATOM N NH1 -0.47 ! |
> > 04ATOM HN H 0.31 ! HN-N
> > 05ATOM CA CT1 0.07 ! | HB1
> > 06ATOM HA HB 0.09 ! | /
> > 07GROUP ! HA-CA--CB-HB2
> > 08ATOM CB CT3 -0.27 ! | \
> > 09ATOM HB1 HA 0.09 ! | HB3
> > 10ATOM HB2 HA 0.09 ! O=C
> > 11ATOM HB3 HA 0.09 ! |
> > 12GROUP !
> > 13ATOM C C 0.51
> > 14ATOM O O -0.51
> > 15BOND CB CA N HN N CA
> > 16BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
> > 17DOUBLE O C
> > 18IMPR N -C CA HN C CA +N O
> > 19DONOR HN N
> > 20ACCEPTOR O C
> > 21IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
> > 22IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
> > 23IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
> > 24IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
> > 25IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
> > 26IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
> > 27IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
> > 28IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
> > 29IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
> > 30IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
> >
> > Line 01: 0.00 is the charge of the residue?
> > Line 03: -0.47 is ?
> > Line 02,07,12: Why need to have this line?
> > Line 15,16: Why need two line for bond? What is C +N? is it carbonyl carbon to the N of another residue?
> > Line 18: Totally no idea.
> > Line 21 to 30: * is?
> > Line 21: 1.3551 126.4900 180.0000 115.4200 0.9996
> > 1.3551=bond length? 126.4900=angle? 180.0000=dihedral angle?
> > what is the last two?(115.4200 and 0.9996)
> > Line 21 to 30: How to look at the oder of the element?
> > for example, Line 28 is continuing, others just like jumping around.
> >
> > Many many thanks.
> >
> > --
> > Chai Ann NG (Andy)
> > Department of Chemistry
> > La Trobe University
> > Victoria 3086
> > Australia
> > --
> >
>
>
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>
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