AMBER Archive (2005)

Subject: Re: AMBER: An atom name with 4 characters is not compatible with Leap ?

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 27 2005 - 12:39:08 CDT

On Wed, Jul 27, 2005, Arnoult, Eric [PRDFR] wrote:
>
> I construct the pdb file with the following command lines :
>
> ${AMBHOME}/antechamber -i ${MOL}.ac -fi ac -o ${MOL}.mpdb -fo mpdb -j 5 -s 2
> -rn ${MOL}

OK...there does seem to be a a bug in the way antechamber outputs its pdb files.
For the moment, save things in antechamber as mol2 format (which you can load
into LEaP), and have LEaP or ambpdb create pdb files if you need them.

Thanks for reporting this...we'll see if we can get it fixed.

...regards...dac

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