On Mon, Sep 9, 2013 at 3:20 AM, 张明焜 <zhangmk69.gmail.com> wrote:
> 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?
>
I have no idea what format the file you posted is, but what you need to do
now is to convert that file to a PDB. Then you can use antechamber with
that PDB to generate the library files that tleap needs to create a prmtop.
You can use OpenBabel or something to convert the file. antechamber will
_not_ create a PDB OR a prmtop file for you. It will take a PDB and
generate a force field library (e.g., mol2, Amber prep; basically anything
that has the charges defined). tleap can then take that library file and
help you create a prmtop.
I assure you, tutorial B4 is about as detailed an explanation of how to use
antechamber as you can get, so I suggest reading through the tutorial and
trying to understand what each step is doing and why that step is
necessary. If you have more questions, try to be as specific as possible,
since your current question is far too general to help us understand how to
help.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 06:30:03 PDT
