AMBER Archive (2006)

Subject: Re: AMBER: xleap problems

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Dec 04 2006 - 09:46:34 CST

Hi,

It sounds like you need to preload in leap required parameters (frcmod) and library (mol2 or OFF) for your new residue, then you should try loading your pdb file.

regards,

jenk

anna.schrey_at_gmx.de wrote: Dear amber community,

I am using new parameterised residues, one of which causing problems. When I try to read an pdb file containing this residue which has been generated using ambpdb, into xleap, xleap crashes and I get error messages as follows:

fenix 54% !FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 121
!FATAL: Message: Atom CT1 is not in the first list
!
!ABORTING.

This does not happen if I read in a pdb file which contains the new residue only.

What might be the problem?

best regards,

Anna 

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   Cenk Andac, M.S., Ph.D. Student
 
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