I attached wrong LYA.mol2 file, but I have still errors about parameters...
/Urszula
_______
Von: case [case.biomaps.rutgers.edu]
Gesendet: Dienstag, 15. Mai 2012 15:07
An: AMBER Mailing List
Betreff: Re: [AMBER] problems with added hydrogens to non standard residue
On Tue, May 15, 2012, Urszula Uciechowska wrote:
>
> I developed a lib for a terminal Lysine residue, LYA.mol2. However after
> loading everything together with the peptide.pdb I have still errors
> regarding the parameters,
> I attached the files:
>
> LYA.mol2 - terminal Lysine
This file has atom types that are just "H", "N", "C", etc. These don't
correspond to any atom types that Amber or gaff know about.
> leap.log
The error in this file is in lines like this:
Unit Editor: Could not find bond parameter for: C - H
Basically, Amber doesn't have parameters for the atom types you have in the
LYA.mol2 file. You probably need to generate this residue in a way that uses
atom types Amber understands.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 15 2012 - 06:30:04 PDT
