You need an input line like the following in LEaP to add a new atom type:
addAtomTypes {{ "O3" "O" "sp3" }}
Hard to tell if you've done this from your message.
G'luck!
Kristina
>===== Original Message From Layi Adekoya <adekoya.fagmed.uit.no> =====
>Hello,
>I need help!!
>I am trying to modell an unnatural amino acid.
>A charged serine (that has lost it's hydrogen)
>I have built it with leap. I have an unstandard
>residue type. I have specified the new type as '03'.since the oxygen
>ceases to be the usual hydroxyl oxygen.
>Leap is however complaining saying the new type not found.
>What do I do to help leap accept this new type?
>I am using amber7.
>
>Help will be greatly appreciated.
>
>Layi
****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse.structbio.vanderbilt.edu
Received on Fri May 23 2003 - 00:53:00 PDT
