AMBER Archive (2009)

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

From: sarvin moghaddam (moghaddam_at_umbi.umd.edu)
Date: Thu Jan 29 2009 - 09:24:50 CST

Hi,

When I use the script below:

source leaprc.gaff
m = loadmol2 test.mol2
saveamberparm m test.top test.xyz

and

save it as test.lrc, then

tleap < test.lrc

I get:
*
*** Error: getline(): not interactive, use stdio.

*I really appreciate if let me know if the source of the error!
Thank in advance,

Sarvin*
*

Wei Zhang wrote:
> 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
>
>

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