Hi, i'm newbie in using amber suite.. now i'm using amber 11..
I want to ask how to make prmtop and inpcrd for the ligand that drawn by our self? I drawn the ligand using symyx draw, the output file is .mol, here is the file:
SMMXDraw02141214502D
29 32 0 0 0 0 0 0 0 0999 V2000
11.6762 -12.1694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.1058 -12.1690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.3924 -11.7562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.1058 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6762 -12.9997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.3942 -13.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.8220 -11.7555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.5382 -12.1690 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
14.5382 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.8220 -13.4095 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
13.8220 -10.9285 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
15.2545 -11.7555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2545 -10.9285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.9707 -12.1690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6869 -11.7555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.9707 -10.5149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6869 -10.9285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2545 -13.4095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.9707 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6869 -13.4095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.4031 -12.9960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.1193 -13.4095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.1193 -14.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.8355 -14.6500 0.0000 S 0 0 3 0 0 0 0 0 0 0 0 0
17.4031 -14.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6869 -14.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.5518 -14.2365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
18.8355 -15.4770 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
19.5518 -15.0635 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6 4 1 0 0 0 0
5 6 2 0 0 0 0
2 3 1 0 0 0 0
1 5 1 0 0 0 0
4 2 2 0 0 0 0
3 1 2 0 0 0 0
2 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
4 10 1 0 0 0 0
7 11 2 0 0 0 0
8 12 1 0 0 0 0
12 13 2 0 0 0 0
12 14 1 0 0 0 0
14 15 2 0 0 0 0
13 16 1 0 0 0 0
16 17 2 0 0 0 0
9 18 1 0 0 0 0
18 19 2 0 0 0 0
19 20 1 0 0 0 0
20 21 2 0 0 0 0
21 22 1 0 0 0 0
22 23 2 0 0 0 0
23 24 1 0 0 0 0
23 25 1 0 0 0 0
25 26 2 0 0 0 0
24 27 2 0 0 0 0
24 28 2 0 0 0 0
24 29 1 0 0 0 0
17 15 1 0 0 0 0
20 26 1 0 0 0 0
M END
when i want to use command reduce to add all the hydrogen atoms to the mole file, why it was different from the antechamber tutorial by ross walker and sishi tang? is it different when we want to use ligand file between file that we drawn by ourself using symyx draw and file from www.pdb.org?
please reply this messages.. thanks..
sincerely, Ajid
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Received on Tue Feb 21 2012 - 20:30:02 PST
