Hi,
No, you cannot do that. You must go through leap (tleap or sleap).
1. you can use antechamber to generate a mol2 file
antechamber -i test.mol -fi mol -o test.mol2 -fo mol2
the generated mol2 file will have charge amber and atom type
2. use leap to load the generated mol2 file, and generate top file
you need write a script like the following:
source leaprc.gaff
m = loadmol2 test.mol2
saveamberparm m test.top test.xyz
save it as test.lrc, then
sleap < test.lrc
Sincerely,
Wei
On Jan 28, 2009, at 1:49 PM, sarvin moghaddam wrote:
> Hi,
>
> I was wondering if I can generate the top file using antechamber
> having the mol file. I know it should sound very trivial for Amber
> users but I am a beginner and have read all the antechmaber related
> parts in Amber manual and also the paper by Case et. al. But still
> was wondering if I only can get the top file by:
>
> antechamber -i test.mol -fi mol -o test.? -fo ?
>
> I have the mol file generated by ACD/ChemSketch
>
> Appreciate your help.
>
> Thanks!
> Sarvin
>
>
>
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Received on Fri Jan 30 2009 - 01:30:14 PST
