Dear Aditya Setiajid,
I wonder if you drew your molecule and consequently generated a
structure in 2 dimensions (2D)... I would construct a structure in 3D
using xLEaP from AmberTools, using Javaapplet & Jmol, using whatever
existing tool etc...
for LEaP, you should generate a PDB file format for your input PDB
molecule. I do not think LEaP does understand the mol fle format.
regards, Francois
> 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?
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Received on Tue Feb 21 2012 - 22:30:02 PST
