AMBER Archive (2009)

Subject: Re: [AMBER] generating top file using antechmaber

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Wed Jan 28 2009 - 14:12:20 CST

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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