Thank you professor!
According to you,I download a coordinates file of melamine(C3H6N6) like
below:
AX2
CCTOOLS-1221121131
15 15 0 0 0 0 0 0 0 0999 V2000
0.0180 -1.3290 0.0010 C 0 0 0 0 0
1.1420 0.6800 -0.0020 C 0 0 0 0 0
-1.1600 0.6490 -0.0020 C 0 0 0 0 0
0.0370 -2.7090 0.0010 N 0 0 0 0 0
-2.3650 1.3230 0.0010 N 0 0 0 0 0
-0.0180 1.3290 0.0010 N 0 0 0 0 0
2.3280 1.3870 0.0010 N 0 0 0 0 0
1.1600 -0.6490 -0.0020 N 0 0 0 0 0
-1.1420 -0.6800 -0.0020 N 0 0 0 0 0
0.8830 -3.1830 -0.0010 H 0 0 0 0 0
-0.7970 -3.2060 0.0040 H 0 0 0 0 0
-2.3780 2.2930 0.0050 H 0 0 0 0 0
-3.1980 0.8260 -0.0010 H 0 0 0 0 0
2.3150 2.3560 0.0050 H 0 0 0 0 0
3.1740 0.9130 -0.0010 H 0 0 0 0 0
1 4 1 0 0 0
1 8 2 0 0 0
1 9 1 0 0 0
2 6 2 0 0 0
2 7 1 0 0 0
2 8 1 0 0 0
3 5 1 0 0 0
3 6 1 0 0 0
3 9 2 0 0 0
4 10 1 0 0 0
4 11 1 0 0 0
5 12 1 0 0 0
5 13 1 0 0 0
7 14 1 0 0 0
7 15 1 0 0 0
M END
$$$$
and I learned antechamber in Tutorial B4. Tutorial B4 illuminated how to
generate a ligand PDB from its protein with antechamber,and there is
no enough explanation about antechamber in "AmberTools12" .So could you
please give me a more detailed method to generate a PDB or Prmtop file with
antechamber?
thanks
On Fri, Sep 6, 2013 at 8:31 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Sep 06, 2013, 张明焜 wrote:
>
> > I am a amber beginer,I know the prmtop and inpcrd files of a protein can
> be
> > produced by a ready PDB file ,but how can I get the prmtop and inpcrd
> files
> > of a small molecule like melamine(H2N-CH2-COOH) which has not a ready PDB
> > file ?
>
> If you have coordinates in some format, you would need to convert it to PDB
> format. If you don't have any coordinates, you can use programs like
> ChemDraw
> or xleap to draw the molecule on the screen and create coordinates.
>
> Once you have a set of coordinates, you will need to use antechamber to
> generate a force field: see Tutorial B4 for an example.
>
> Finally, melamine is C3H6N6, and is nothing like the molecule you describe
> above. What you wrote is a gas-phase version of glycine.
>
> ....dac
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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ZhangMK
+8623-63063582
Chongqing Institute of Green and Intelligent Technology of Chinese Academy
Sciences.
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Received on Mon Sep 09 2013 - 00:30:03 PDT
