VMD-L Mailing List
From: KIRTANA S (skirtana4_at_gmail.com)
Date: Thu May 21 2009 - 12:32:35 CDT
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If I use topotools plugin with scripts as suggested in your mail ,what
should I replace for the index numbers . I am a first time user and non able
to decide on it .Can you suggest an example if my psf file is :
PSF
1 !NTITLE
REMARKS VMD generated structure x-plor psf file
24 !NATOM
1 2 MOL AU13 AU13 0.000000 196.9666 0
2 2 MOL AU14 AU14 0.000000 196.9666 0
3 2 MOL AU17 AU17 0.000000 196.9666 0
4 2 MOL AU17 AU17 0.000000 196.9666 0
5 2 MOL AU18 AU18 0.000000 196.9666 0
6 2 MOL AU18 AU18 0.000000 196.9666 0
7 2 MOL AU18 AU18 0.000000 196.9666 0
8 2 MOL AU19 AU19 0.000000 196.9666 0
9 2 MOL AU1 AU1 0.000000 196.9666 0
10 2 MOL AU1 AU1 0.000000 196.9666 0
11 2 MOL AU1 AU1 0.000000 196.9666 0
12 2 MOL AU1 AU1 0.000000 196.9666 0
13 2 MOL S13 S13 0.000000 32.0650 0
14 2 MOL C38 C38 0.000000 12.0107 0
15 2 MOL C40 C40 0.000000 12.0107 0
16 2 MOL C41 C41 0.000000 12.0107 0
17 2 MOL C42 C42 0.000000 12.0107 0
18 2 MOL C43 C43 0.000000 12.0107 0
19 2 MOL C44 C44 0.000000 12.0107 0
20 2 MOL H51 H51 0.000000 1.0079 0
21 2 MOL H53 H53 0.000000 1.0079 0
22 2 MOL H55 H55 0.000000 1.0079 0
23 2 MOL H57 H57 0.000000 1.0079 0
24 2 MOL H59 H59 0.000000 1.0079 0
13 !NBOND: bonds
6 13 13 14 14 19 14 15
15 20 15 16 16 17 16 21
17 18 17 22 18 23 18 19
19 24
0 !NTHETA: angles
0 !NPHI: dihedrals
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
1 0 !NGRP
0 0 0
I need to add the bond for Au and bond angles in the file .
Thanks and regards
kirtana
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