Hi Sook,
I think that leap doesn't know how to deal with the "LIG" residue. Could you provide your leap input file? If LIG is a ligand you should get parameters for it. Take a look at tutorial B4 (Amber website) on how to use the antechamber tools to parametrize a ligand. Then, you should include them in your leap input file to get prmtop and inpcrd files of the complex.
Best,
Aldo =======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer BiologyCancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
=========================================
De: "Wong, Sook (NIH/NCATS) [V]" <sook.wong.nih.gov>
Para: "amber.ambermd.org" <amber.ambermd.org>
Enviado: Martes, 9 de diciembre, 2014 16:59:01
Asunto: [AMBER] TLEAP issues
Hi,
I am trying to generate prmtop & inpcrd using tleap. However, I am encountering the following issues:
FATAL: Atom .R<LIG 393>.A<C1 1> does not have a type.
FATAL: Atom .R<LIG 393>.A<C2 2> does not have a type.
FATAL: Atom .R<LIG 393>.A<C3 3> does not have a type.
FATAL: Atom .R<LIG 393>.A<C4 4> does not have a type.
FATAL: Atom .R<LIG 393>.A<C5 5> does not have a type.
FATAL: Atom .R<LIG 393>.A<C6 6> does not have a type.
FATAL: Atom .R<LIG 393>.A<C7 7> does not have a type.
FATAL: Atom .R<LIG 393>.A<C8 8> does not have a type.
FATAL: Atom .R<LIG 393>.A<C9 9> does not have a type.
FATAL: Atom .R<LIG 393>.A<C10 10> does not have a type.
FATAL: Atom .R<LIG 393>.A<C11 11> does not have a type.
FATAL: Atom .R<LIG 393>.A<C12 12> does not have a type. Etc.
I have enclosed the log from tleap as well as my com.pdb. Can anyone advise the issue?
-Sook
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Received on Wed Dec 10 2014 - 07:30:02 PST
