Thanks! The ligand is sildenafil. When I use:
antechamber -i sid.out -fi gout -o sid.prep -fo prepi -c resp
and
parmchk -i sid.prep -f prepi -o sid.frcmod
There is not any ATTN REVISION information in the sid.frcmod file. But When I load the parameters to my PDB file, the system always tell me there is one unknown element. So I have to use the fllowing order:
antechamber -i sid.out -fi gout -o sid.prep -fo prepi -c resp -at amber
and
parmchk -i sid.prep -f prepi -o sid.frcmod
This time there is many ATTN REVISION in the sid frcmod. Such as:
SO 0.000 0.000 ATTN, need revision
CA-SO 0.00 0.000 ATTN, need revision
SO-O 0.00 0.000 ATTN, need revision
SO-NT 0.00 0.000 ATTN, need revision
CA-SO-O 0.000 0.000 ATTN, need revision
CA-SO-NT 0.000 0.000 ATTN, need revision
SO-NT-CT 0.000 0.000 ATTN, need revision
O -SO-O 0.000 0.000 ATTN, need revision
O -SO-NT 0.000 0.000 ATTN, need revision
CA-SO-NT-CT 1 0.000 0.000 0.000 ATTN, need revision
SO-NT-CT-H1 1 0.000 0.000 0.000 ATTN, need revision
SO-NT-CT-CT 1 0.000 0.000 0.000 ATTN, need revision
O -SO-NT-CT 1 0.000 0.000 0.000 ATTN, need revision
Thanks for your help!
> On Mon, Apr 18, 2005, ?????? wrote:
>
> > I have a ligand molecule which has a sulphur element. There is two S=O
> > bonds in this molecule. But there is not parameter of SO in AMBER. How
> > can I get its parameter?
>
> We would need more details to be of help. What exactly is the molecule? What
> did you try, and what happened?
>
> ....dac
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Received on Tue Apr 19 2005 - 03:53:00 PDT
