AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber ligand prep

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Jan 27 2009 - 09:34:25 CST

On Jan 27, 2009, at 9:24 AM, George Tzotzos wrote:

> Hi David and David
>
> Many thanks for the suggestion today and yesterday. I did try almost
> everything. I prepared de nove the ligand in Chimera. I'm attaching
> the file. I don't see anything wrong with connectivities or
> formating. Antechamber still refuses to accept the connectivity "1
> is not a valid atom id in CONECT 1 2 3 4". I'm attaching
> the new ligand file in case you can see something that I miss.

I'm not sure what your problem is now.
babel converts this new pdb fine, and
     antechamber -i new.pdb -fi pdb -o new.prepin -fo prepi -s 2
works fine for me (with Amber 9). 

--
David Watson • Graduate Student • Medicinal Chemistry • 425 Faser Hall  
• University MS  38677 • 1.662.915.1663

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