AMBER Archive (2003)

Subject: Re: leap complains!

From: Jose Ramon Blas (jramon_at_ub222059.pcb.ub.es)
Date: Thu May 22 2003 - 17:03:02 CDT

Hi,
you should define the atom_type of your new atom in a parameter file and
load it previously in leap by "loadamberparams".

Hope this helps,

Blas

---------------------------------------------------------------------------
Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon_at_mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona

On Thu, 22 May 2003, Layi Adekoya wrote:

>
> 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
>
>