Urszula,
> I attached wrong LYA.mol2 file, but I have still errors about parameters...
For LYA.mol2:
you need to define a new atom type for the aldehydic hydrogen
create a frcmod file with this aldehyde hydrogen. I wonder if K.
Kirschner has a FF, that handles aldehyde hydrogens...
For the PDB file:
- rename the LYS residue name into LYA
- rename the LS atom names in agreement with these in LYA.mol2
regards, Francois
> _______
> 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
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Received on Tue May 15 2012 - 07:00:04 PDT
